F on ie s in Mic obiology 01 on ie sin.o g
CyanoCyc cyanobac e ial web
po al
Lisa R.Moo e
1
*, RonCaspi
1, DouglasA.Campbell
2,
JohnR.Casey
3, SophieC e ecoeu
4, Da idJ.Lea-Smi h
5,
BinLong
6, NaamanM.Oma
2, SuzanneM.Paley
1,
NicolasM.Schmelling
7, Alejand oTo ado
8, Jona hanP.Zeh
9
and Pe e D.Ka p
1
*
1 SRI In e na ional, Menlo Pa k, CA, Uni ed S a es, 2 Moun Allison Uni e si y, Sack ille, NB, Canada,
3 Law ence Li e mo e Na ional Labo a o y, Physical and Li e Sciences Di ec o a e, Li e mo e, CA,
Uni ed S a es, 4 Wa e shed Hyd ology and Ecology Resea ch Di ision, En i onmen and Clima e
Change Canada, Bu ling on, ON, Canada, 5 School o Biological Sciences, Uni e si y o Eas Anglia,
No wich, Uni ed Kingdom, 6 Depa men o Plan Pa hology and Mic obiology, Texas A&M Uni e si y,
College S a ion, TX, Uni ed S a es, 7 K au s and Sp ou s, Duesseldo , Ge many, 8 Ins i u e o Plan
Biochemis y and Pho osyn hesis, Uni e si y o Se ille and Spanish Na ional Resea ch Council, Se illa,
Spain, 9 Ocean Sciences Depa men , Uni e si y o Cali o nia, San a C uz, San a C uz, CA, Uni ed S a es
CyanoCyc is a web po al ha in eg a es an excep ionally ich da abase
collec ion o in o ma ion abou cyanobac e ial genomes wi h an ex ensi e
sui e o bioin o ma ics ools. I was de eloped o add ess he needs o he
cyanobac e ial esea ch and bio echnology communi ies. The 277 anno a ed
cyanobac e ial genomes cu en ly in CyanoCyc a e supplemen ed wi h
compu a ional in e ences including p edic ed me abolic pa hways, ope ons,
p o ein complexes, and o hologs; and wi h da a impo ed om ex e nal
da abases, such as p o ein ea u es and Gene On ology (GO) e ms impo ed
om UniP o . Fi e o he genome da abases ha e unde gone manual cu a ion
wi h inpu om mo e han a dozen cyanobac e ia expe s o co ec e o s
and in eg a e in o ma ion om mo e han 1,765 published a icles. CyanoCyc
has bioin o ma ics ools ha encompass genome, me abolic pa hway and
egula o y in o ma ics; omics da a analysis; and compa a i e analyses,
including isualiza ions o mul iple genomes aligned a o hologous genes,
and compa isons o me abolic ne wo ks o mul iple o ganisms. CyanoCyc
is a high-quali y, eliable knowledgebase ha accele a es scien is s’ wo k by
enabling use s o quickly ind accu a e in o ma ion using i s powe ul se o
sea ch ools, o unde s and gene unc ion h ough expe mini- e iews wi h
ci a ions, o acqui e in o ma ion quickly using i s in e ac i e isualiza ion ools,
and o in o m be e decision-making o undamen al and applied esea ch.
KEYWORDS
CyanoCyc, cyanobac e ia, genomes, me abolism, bioin o ma ics, da abase, cu a ion,
bio echnology
In oduc ion
Cyanobac e ia a e some o he oldes , mos di e se and ecologically impo an mic obial
pho o ophs on Ea h. Wi h he apid de elopmen o genomic ools applied o cyanobac e ial
esea ch and he g owing in e es in cyanobac e ia as sou ces o ma ke able seconda y
me aboli es and as ca bon-neu al, bioenginee ing pla o m o ganisms, he e is an inc easing
need o eliable knowledgebase da abases. Un o una ely, he long- e m main enance o such
OPEN ACCESS
EDITED BY
Jana Sei e ,
Uni e si y o Hohenheim, Ge many
REVIEWED BY
Ruben Michael Ceballos,
Uni e si y o Cali o nia, Me ced,
Uni edS a es
Joon-Yong Lee,
P ognomiQ Inc, Uni edS a es
*CORRESPONDENCE
Lisa R. Moo e
[email p o ec ed]
Pe e D. Ka p
pe e [email p o ec ed]
RECEIVED 17 No embe 2023
ACCEPTED 11 Janua y 2024
PUBLISHED 31 Janua y 2024
CITATION
Moo e LR, Caspi R, Campbell DA, Casey JR,
C e ecoeu S, Lea-Smi h DJ, Long B,
Oma NM, Paley SM, Schmelling NM,
To ado A, Zeh JP and Ka p PD (2024)
CyanoCyc cyanobac e ial web po al.
F on . Mic obiol. 15:1340413.
doi: 10.3389/ micb.2024.1340413
COPYRIGHT
© 2024 Moo e, Caspi, Campbell, Casey,
C e ecoeu , Lea-Smi h, Long, Oma , Paley,
Schmelling, To ado, Zeh and Ka p. This is an
open-access a icle dis ibu ed unde he
e ms o he C ea i e Commons A ibu ion
License (CC BY). The use, dis ibu ion o
ep oduc ion in o he o ums is pe mi ed,
p o ided he o iginal au ho (s) and he
copy igh owne (s) a e c edi ed and ha he
o iginal publica ion in his jou nal is ci ed, in
acco dance wi h accep ed academic
p ac ice. No use, dis ibu ion o ep oduc ion
is pe mi ed which does no comply wi h
hese e ms.
TYPE Technology and Code
PUBLISHED 31 Janua y 2024
DOI 10.3389/ micb.2024.1340413
Moo e e al. 10.3389/ micb.2024.1340413
F on ie s in Mic obiology 02 on ie sin.o g
da abases has been a challenge. Fo ins ance, CyanoBase (Nakao e al.,
2010; Fujisawa e  al., 2017), he cen al knowledgebase o he
cyanobac e ial communi y, is equen ly una ailable and has limi ed
bioin o ma ics ools. In addi ion, i is well-known ha unding o
li e-science da abases o en ceases a e a limi ed ime-pe iod, hus
unde mining he long- e m iabili y o hese esou ces.
The lack o in o ma ion ega ding cyanobac e ial genomics, as
well as conce ns o e he ins abili y o many dispa a e bioin o ma ics
esou ces inspi ed a ound able discussion a he 14 h Wo kshop on
Cyanobac e ia, which ook place a Michigan S a e Uni e si y in June
2022, and an ad hoc commi ee was o med o explo e al e na i es.
A e mon hs o discussion, he commi ee ecommended
de elopmen o a new cyanobac e ial da abase collec ion in eg a ed
wi h bioin o ma ics ools o se e he communi y’s needs. CyanoCyc
– a cyanobac e ial da abase po al ha esides wi hin he la ge , well-
es ablished BioCyc collec ion (Ka p e al., 2019) – was de eloped, and
he commi ee was e-de ined o se e as an Ad iso y Boa d,
p o iding in aluable inpu du ing CyanoCyc’s implemen a ion.
The CyanoCyc web po al couples a ich collec ion o
cyanobac e ial genome da abases wi h powe ul and easy- o-use
bioin o ma ics ools o enable s udies o cyanobac e ia om molecules
o me abolic models, and om basic biology o syn he ic biology.
CyanoCyc con ains 277 cyanobac e ial genomes ac oss 56 gene a and
co e s a as ange o pheno ypic ypes, om soils o eshwa e and
he ma ine en i onmen . Fi e o he da abases, Synechocys is sp. PCC
6803 subs . Kazusa, Synechococcus elonga us PCC 7942, Synechococcus
sp. WH8102, P ochlo ococcus ma inus CCMP1375 (P. ma inus SS120)
and P ochlo ococcus ma inus pas o is CCMP1986 (P. ma inus MED4),
we e u he imp o ed by cu a o s, who manually co ec ed
anno a ion e o s in he genomes and en e ed in o ma ion ga he ed
om mo e han 1,765 publica ions (Table1). The cu a ed in o ma ion
anges om expe imen ally elucida ed gene unc ions o egula o y
e en s and me abolic pa hways. O e all, he CyanoCyc da abases span
a wide ange o in o ma ion, including gene unc ions; p o ein
complexes; p o ein ea u es; Gene On ology anno a ions (Ashbu ne
e al., 2000); me abolic pa hways, eac ions, and me aboli es; gene
essen iali y da ase s; and egula o y in e ac ions.
By in eg a ing such a di e se ange o in o ma ion ypes,
CyanoCyc sa is ies a la ge se o in o ma ion-seeking needs o
cyanobac e ial scien is s. Fo example, gi en a gene name,
CyanoCyc enables use s o de e mine he unc ion o i s p oduc ,
wha complex, i any, he p oduc pa icipa es in, and e ie e any
cu a ed egula o y in luences on he gene and i s p oduc . I he
gene encodes an enzyme, CyanoCyc iden i ies eac ions he
enzyme ca alyzes and he pa hway(s) in which hese eac ions
pa icipa e. O hologs o he gene in o he o ganisms can
be eadily iden i ied and compa ed.
CyanoCyc also con ains a la ge numbe o bioin o ma ics ools
ha a e in eg a ed wi h all he genome da abases and simpli y access
o in o ma ion, p oduce isual ou pu s, and pe o m mul iple
compu a ional analyses. As pa o he BioCyc collec ion, use s also
ha e access o he mo e han 20,000 mic obial da abases, making he
bioin o ma ics ools e en mo e use ul. Some o hese ools (all
CyanoCyc ools a e also p esen in BioCyc), comp ise:
• Sea ches ha enable use s o quickly ind desi ed in o ma ion,
including:
◦ Boolean sea ches, e.g., ind all genes in a gi en egion o he
ch omosome whose p oduc s lie in a gi en molecula -weigh
ange and a e ound in he memb anes
◦ Ve y as single-o ganism BLAST sea ches
◦ Sequence pa e n sea ches
• A genome b owse ha enables g aphical explo a ion o he
genome and compa isons ac oss mul iple genomes
• A me abolic ne wo k b owse ha enables explo a ion o
pa hways and me abolic capabili ies
• A sui e o omics-da a analysis ools ha enables quick and no el
analyses o ansc ip omics, p o eomics, and me abolomics da a
• Va ious ools o be ween-da abase compa isons
• Sma Tables ha allow analy ical sp eadshee capabili ies linked
o in o ma ion wi hin BioCyc and he abili y o b ing in you
own da a, e.g., omics da a, sha ed and expo ed in o ma ion
• A eedback ool ha enables use s o sugges da abase co ec ions
and upda es
In his pape , wedesc ibe he me hodology o c ea ion o he new
da abases, he manual cu a ion p ocess by in-house cu a o s and
cyanobac e ia communi y expe s, he enhancemen s o in o ma ion
p esen a ion and bioin o ma ics ools inspi ed by he Ad iso y Boa d,
and he p opaga ion o o holog-based in o ma ion o addi ional
cyanobac e ial genomes. Wealso p esen examples o wha ypes o
esea ch can bepe o med wi h he bioin o ma ics ools a ailable
h ough CyanoCyc and BioCyc as a whole.
We add ess he sus ainabili y o CyanoCyc by o e ing he websi e
h ough a subsc ip ion model. E en wi h a sequenced genome in hand,
ou knowledge o gene unc ion, me abolism, egula ion, and o he
aspec s o he cyanobac e ia un olds o e a ime pe iod o decades. Wi h
he las upda e o CyanoBase occu ing in 2017 (Fujisawa e al., 2017),
TABLE1 The i e manually cu a ed da abases in CyanoCyc and some s a is ics on hei con en .
Synechocys is Synechococcus
elonga us PCC 7942
Synechococcus sp.
WH 8102
P. ma inus
SS120
P. ma inus
MED4
Genome size 3,956,956 2,750,104 2,434,428 1,751,080 1,657,990
Genes 3,679 2,772 2,578 1,931 1,840
Pa hways 256 243 219 191 234
Publica ions 1,028 422 184 76 55
Summa ies 384 216 234 115 154
Genes and Pa hways: Coun s o genes and pa hways in each da abase. Publica ions a e he numbe o publica ions ci ed in and unique o each da abase, om which da a we e cu a ed.
Summa ies quan i ies he cu a o -au ho ed summa y in o ma ion, as ex book-page-equi alen s, in each da abase. A epo ha includes addi ional poin s o compa ison is a ailable om he
BioCyc Compa a i e Analysis ool. Da a is om BioCyc e sion 27.1, eleased on Augus 28, 2023.
Moo e e al. 10.3389/ micb.2024.1340413
F on ie s in Mic obiology 03 on ie sin.o g
and wi h he g adual decay in ope a ional i ness o CyanoBase, he
di icul y o main aining and sus aining da abases o e long pe iods o
ime is e iden . Fo many yea s he Na ional Science Founda ion (NSF)
unded mos da abase g an s o only a single g an cycle. NSF did und
he TAIR (The A abidopsis In o ma ion Resou ce) da abase o mul iple
g an cycles. E en ually NSF phased ou TAIR’s unding, compelling
hem o shi o a subsc ip ion model, which has been success ul o
mo e han a decade (Check Hayden, 2013; Reise e al., 2016). Like
TAIR, BioCyc con e ed o a subsc ip ion model in 2016. Because
BioCyc suppo s genome da abases o a wide se o bac e ia, including
he cyanobac e ia wi hin he CyanoCyc po al, BioCyc is able o sp ead
many o i s cos s, such as websi e ope a ions, ac oss a la ge use
communi y, hus keeping o e all subsc ip ion p ices ela i ely low.
Gi en ha no o he high-quali y, in eg a ed da abase o he
cyanobac e ia has eme ged and been main ained since he i s
cyanobac e ium was sequenced 27 yea s ago (Kaneko e al., 1996),
wehope he communi y will suppo he CyanoCyc subsc ip ion model
o sus ainabili y.
Me hods
This sec ion desc ibes he me hods used o c ea e and cu a e new
CyanoCyc Pa hway/Genome Da abases (PGDBs). To cons uc each
da abase, an anno a ed genome was impo ed om Re Seq (O'Lea y e al.,
2016) and en iched by impo ing addi ional in o ma ion om o he
da abases, such as p o ein ea u es om UniP o KB (UniP o Conso ium,
2023), and by unning a se ies o compu a ional in e ences s o ed in he
da abase o p oduce esul s, such as compu a ional p edic ion o
me abolic pa hways om i s sequenced genome. Wecollabo a ed wi h
cyanobac e ia esea ch expe s on he manual cu a ion p ocess and o
make enhancemen s o BioCyc bioin o ma ics ools.
C ea ing new CyanoCyc da abases
In BioCyc pa lance, a Tie 3 PGDB is one ha is pu ely
compu a ionally gene a ed; a Tie 2 da abase is manually cu a ed a e
i is gene a ed; and a Tie 1 da abase includes a leas a 1-pe son-yea
o cu a ion, and some imes much mo e. Fo example, ou EcoCyc
da abase o E. coli K-12 has unde gone se e al pe son-decades o
cu a ion based on in o ma ion de i ed om mo e han 42,000
publica ions (Ka p e al., 2023).
C ea ion o an uncu a ed (Tie 3) CyanoCyc da abase begins wi h
compu a ional inges ion o a Re Seq anno a ed genome ollowed by a
se ies o compu a ional in e ences. Se e al componen s o SRI’s
Pa hway Tools so wa e (Ka p e  al., 2021) we e used o p edic
addi ional in o ma ion a ailable in he da abase:
• P edic ed me abolic eac ions and pa hways we e impo ed om
he Me aCyc e e ence pa hway da abase (Caspi e al., 2020)
• Ope ons we e p edic ed using a combina ion o ea u es
including dis ance and unc ional ela edness be ween
adjacen genes
• P o ein complexes we e p edic ed using keywo d analysis o gene
p oduc names
• T anspo eac ions we e p edic ed om keywo d analysis o
anspo e names
• Pa hway hole ille s (genes whose p oduc s a e p edic ed o
ca alyze pa hway s eps ha cu en ly ha e no associa ed enzyme)
we e p edic ed
• O hologs we e compu ed be ween each p o ein in he o ganism
and he p o eomes o all o he BioCyc o ganisms
• P am domain (Mis y e al., 2021) sea ches we e un ac oss he
p o eome; ma ching domains we e sa ed as p o ein ea u es
A e hese compu a ional p edic ions we e pe o med,
weimpo ed se e al ypes o da a (when a ailable) om UniP o KB
in o he new PGDBs:
• P o ein ea u es such as me al-ion binding si es and enzyme
ac i e si es
• Gene On ology anno a ions
• UniP o KB accession numbe s
• UniP o unc ional anno a ions no p esen in he
Re Seq anno a ion
Addi ionally, links o da abases such as UniP o , AlphaFold
(Jumpe e al., 2021), and NCBI P o ein (Saye s e al., 2022) we e
c ea ed o p o ide access o addi ional in o ma ion no included in
BioCyc Tie 3 PGDBs.
Manual cu a ion and e iew p ocess
The manual cu a ion p ocess is complex and in ol es e o
co ec ion, en y o missing in o ma ion, and esolu ion o con lic s in
he li e a u e. A i s , compu a ionally buil da abases may bee o -
laden. The e a e mul iple easons o he e o s, including inco ec
p o ein unc ional anno a ions in oduced by Re Seq. Fo example,
inco ec anno a ion may include he e m ‘ubiquinone’ o a
cyanobac e ial quinone syn hesis enzyme based on sequence simila i y
o a non-cyanobac e ial enzyme – e en hough cyanobac e ia do no
p oduce ubiquinone. Inco ec in e ences by he PTools so wa e
include a achmen o he w ong eac ions o gene p oduc s, anno a ion
o gene ic eac ions (classes o mul iple eac ions), o p edic ion o
pa hways ha do no exis in he o ganism. Du ing he p ocess o
manual cu a ion, he cu a o s pe o m many asks, some o which a e
no dependen on he li e a u e, and hese include illing in missing
gene names no comp ised in he genome anno a ions, c ea ing p o ein
complexes no p edic ed by PTools; impo ing me abolic pa hways
om Me aCyc ha a e known o exis in he o ganism bu we e no
compu a ionally p edic ed due o missing o inco ec anno a ion; and
co ec ing compu a ionally p edic ed da a such as ansc ip ion uni s
based on con lic ing expe imen al e idence. By a he mos ime-
consuming pa o manual cu a ion is he addi ion o ma e ial ob ained
om he li e a u e: adding new in o ma ion abou gene unc ion,
egula o y in o ma ion, and no el eac ions and pa hways, and w i ing
mini- e iews wi h ci a ions.
All i e Tie 2 cu a ed species we e subjec o a ca e ul manual
cu a ion p ocess. Addi ionally, he mos ecen ly cu a ed da abase o
Synechocys is sp. PCC 6803 was also e iewed o e a 2-mon h pe iod by
a panel o eigh cyanobac e ial esea che s o ensu e high-quali y da a.
An in i a ion o pa icipa e in cu a ing he Synechocys is sp. PCC 6803
genome da abase on CyanoCyc was emailed o o e 600 cyanobac e ia
esea che s who a ended se e al cyanobac e ia- ela ed con e ences and
Moo e e al. 10.3389/ micb.2024.1340413
F on ie s in Mic obiology 04 on ie sin.o g
was pos ed o social media si es o p o ide oppo uni y o a b oad ange
o pa icipan s. The cu a ion e iew panel was selec ed om hose who
exp essed s ong in e es and he abili y o commi he ime o he
cu a ion e iew p ocess. The goals o he e iew panel we e o e iew
p o ein unc ion and pa hway in o ma ion wi hin he da abase, which
he e iewe s iden i ied in a collabo a i e, online mee ing, sugges
speci ic changes and/o addi ional in o ma ion using he “P o ide
Feedback” bu on, and log wha in o ma ion was e iewed in a
sp eadshee so wecould keep ack o he p ocess. The ac ual cu a ion
was pe o med by CyanoCyc cu a o s. The esea che s con ibu ed
expe ise in ields such as biosyn he ic pa hways, elec on anspo
eac ions, pilus o ma ion, and DNA me hyla ion/ es ic ion enzymes.
O holog-based p opaga ion o
anno a ions
Manually cu a ed gene and p o ein da a om he i e Tie 2
cu a ed da abases we e p opaga ed o he co esponding o hologs in
Tie 3 (uncu a ed) da abases o o he cyanobac e ia. This p ocedu e
(Paley e al., 2021) le e ages limi ed cu a ion esou ces ac oss a wide
se o da abases, and he eby aises he quali y o he en i e collec ion.
Se e al measu es we e employed o p o ec agains po en ial e o s.
Fi s ly, da a was only p opaga ed om an o ganism o closely ela ed
o ganisms. Secondly, p opaga ion was pe o med only i ou c i e ia
we e me : he sou ce p o ein had unde gone some manual cu a ion,
as indica ed by a non-compu a ional e idence code o cu a ion c edi ;
a single candida e o holog could beiden i ied in he a ge s ain; he
wo genes had sequence simila i y alue o p <1e-10; and gene leng hs
di e ed by no mo e han 10%.
Fo o holog pai s mee ing all he c i e ia o p opaga ion, he
a ge gene and p o ein names we e upda ed o ma ch he sou ce, wi h
all eplaced alues eco ded as pa o he gene’s his o y isible o use s.
All eac ion and GO e m assignmen s we e p opaga ed. In addi ion,
i he sou ce p o ein was a membe o a complex, he co esponding
complex was c ea ed in he a ge da abase. Finally, any newly
p edic ed pa hways based on he upda ed anno a ions we e impo ed,
and (a e examina ion o he da abase ansac ion log) any manually
dele ed pa hways p edic ed in bo h sou ce and a ge o ganisms based
on he same le el o e idence we e also dele ed om he a ge da abase.
Resul s
Da abases and cu a ion p ocess
The CyanoCyc po al con ains 277 cyanobac e ial genomes
spanning 56 gene a co e ing he ex ensi e mo phological and
ecological di e si y o cyanobac e ia om he oxin-p oducing
eshwa e cyanobac e ium Mic ocys is ae uginosa NIES-843 (Kaneko
e al., 2007) o he soil cyanobac e ium Nos oc calcicola FACHB-389
(Zhu e al., 2017), and o he as -g owing Synechococcus elonga us
PCC 11801 (Jaiswal e al., 2018) o in e es in gene ic enginee ing
applica ions. Weadded se en addi ional genomes ha he Ad iso y
Boa d membe s sugges ed we e pa icula ly use ul o he esea ch
communi y, and wewill add mo e genomes by use eques ia ou
eques o m (URL=h ps://cyanocyc.o g/ eques -new-pgdb.sh ml)
o new genomes. So a , weha e manually cu a ed i e da abases, all
o which desc ibe picocyanobac e ia, including he eshwa e
o ganisms Synechococcus elonga us PCC 7942 and Synechocys is sp.
PCC 6803 subs . Kazusa, and he ma ine o ganisms Synechococcus
sp. WH8102, P. ma inus SS120, and P. ma inu s MED4 (Table1). Bo h
Synechococcus elonga us PCC 7942 and Synechocys is sp. PCC 6803 a e
excep ionally well-s udied model o ganisms and a e commonly used
in me abolic enginee ing (Jaiswal e  al., 2022). Synechococcus sp.
WH8102 is ep esen a i e o o ganisms wi h a high phycou obilin
ch omopho e composi ion ha a e highly abundan in oligo ophic
oceanic wa e s (Scanlan e al., 2009). P. ma inu s is he dominan
pho osyn he ic o ganism in mos opical and empe a e open ocean
ecosys ems. The high-ligh clade I eco ype, P. ma inus MED4, is
cha ac e is ic o he su ace laye , and he low-ligh clade II/III
eco ype, P. ma inus SS120, is ypical o o ganisms adap ed o lowe
ligh condi ions (Bille e al., 2015).
The cu a ion e iew p ocess o he Synechocys is sp. PCC 6803
da abase was ca ied ou by eigh cyanobac e ia expe s who ocused on
many me abolic pa hways, including he En ne -Doudo o and
hyd oca bon biosyn he ic pa hways, such as alkane biosyn hesis;
p o eins and eac ions, such as he pho oac i e o ange ca o enoid
p o ein; he pho osyn he ic elec on anspo eac ions, such as he
pa hway o elec on anspo in he hylakoid memb ane and in he
plasma memb ane; a ious anspo p ocesses, such as he linea
elec on low h ough plas ocyanin; and he pilin p o eins, such as hose
ound in he ype IV pilus. The expe s sugges ed new ex desc ibing
in o ma ion in pee - e iewed publica ions abou p o eins, eac ions,
and pa hways ha we e no ye cu a ed in he da abase, and also
ecommended a ew co ec ions. Fo some opics, he e iewe s eached
ou o o he colleagues o ob ain addi ional in o ma ion. Expe s a e
c edi ed o hei speci ic e iews below he summa ies on he
in o ma ion pages.
In he u u e, weaim o cu a e addi ional cyanobac e ia ha a e
deemed impo an o he undamen al unde s anding o
cyanobac e ial biology, ecology, and po en ial applica ions in
bio echnology. Po en ial candida es include: Nos oc sp. PCC 7120, a
model ni ogen- ixing, he e ocys -con aining s ain (Zeng and Zhang,
2022); Mic ocys is ae uginosa, which o ms ha m ul algal blooms
(Ha ke e al., 2016); A h ospi a pla ensis, comme cially cul i a ed o
i s nu i ional alue as he ood p oduc Spi ulina (Gen sche a e al.,
2023); and Gloeocapsa bi o mis, which causes s eaks and s ains on
monumen s and buildings (Macedo e al., 2009).
Cu a ed da abases
The CyanoCyc Ad iso y Boa d membe s sugges ed wec ea e
publicly accessible Sma Tables (Table2) lis ing CyanoCyc o ganisms
based on hei pheno ypic subg oups (e.g., ilamen ous o ganisms,
he e ocys o me s, e c.). In addi ion, we c ea ed Sma Tables
including he i e cu a ed cyanobac e ia in CyanoCyc (Cyanobac e ia
Lis : Cu a ed Cyanobac e ial Da abases) and a ep esen a i e lis o
he phylogene ically di e se cyanobac e ia ha a e equen subjec s
o publica ion (Cyanobac e ia Lis : Rep esen a i e Cyanobac e ia) o
enable compa isons ac oss a wide se o o ganisms. When pe o ming
Sequence Pa e n Sea ches o CyanoCyc compa a i e ope a ions,
hese Sma Tables can beused o de ine he se o o ganisms. Thus, o
example, one could un a me abolic ne wo k compa ison ac oss he
lis o o ganisms s o ed in he Sma Table “Cyanobac e ia lis :
Ni ogen Fixing o ganisms” using he Compa a i e Analysis ool and
choosing he Pa hways able (Tools > Analysis > Compa a i e
Moo e e al. 10.3389/ micb.2024.1340413
F on ie s in Mic obiology 05 on ie sin.o g
Analysis). Wealso ex ended he Sma Tables acili y so i is possible
o use an “Add P ope y Column” menu o include columns o
pheno ypic p ope ies such as he ae obici y o he o ganism and he
da e he o ganism was collec ed.
O holog-based p opaga ion
We p opaga ed o hologs om he wo P ochlo ococcus da abases
o 16 o he P ochlo ococcus s ains; he Synechocys is da abase o six
o he Synechocys is sp. PCC 6803 and closely ela ed s ains, he
Synechococcus elonga us PCC 7942 o ou o he Synechococcus
elonga us and closely ela ed s ains; and he Synechococcus sp.
WH8102 o ou ma ine Synechococcus s ains (Table 3). The
p opaga ed genes include a numbe o cases in which unc ions we e
in e ed o genes o p e iously unknown unc ion. Fo example, in
he uncu a ed da abase o Synechocys is sp. PCC 6714, gene RS07570
was p e iously anno a ed simply as “hypo he ical p o ein.” A e
p opaga ion om i s o holog in Synechocys is sp. PCC 6803 Kazusa,
gene RS08070, he p e iously hypo he ical p o ein acqui ed he name
e3, he unc ion ocophe ol cyclase, and wo associa ed eac ions,
which illed p e ious holes in he i amin E biosyn hesis pa hway in
Synechocys is sp. PCC 6714. The co esponding gene page
(URL=h ps://biocyc.o g/gene?o gid=GCF_000478825&id=D082_
RS07570) includes an o holog link and shows he summa y
desc ip ion om he o holog in he sou ce da abase, as well as i s
his o y o upda es.
Communi y-d i en da abase
enhancemen s
A he sugges ion o he CyanoCyc Ad iso y Boa d membe s,
we made mul iple enhancemen s o CyanoCyc. We c ea ed he
CyanoCyc.o g home page and an In oduc ion o CyanoCyc page ha
con ains in o ma ion abou he da abases and ools and p o ides links
o o he cyanobac e ial esou ces. Weadded he ca boxysome o he
cellula compa men on ology used in he da abases o mo e
accu a ely depic ca boxysome-associa ed eac ions and pa hways. To
accommoda e he ongoing changes o cyanobac e ial axonomic
nomencla u e and enable g ea e ease in inding cyanobac e ial
species based on olde (and o en mo e commonly used) names, he
Ad iso y Boa d iden i ied such names o many cyanobac e ial
species. These olde names a e lis ed on each o ganism’s Summa y
S a is ics (“home”) page and can beused when selec ing a da abase
(e.g., “Nos oc a iabilis ATCC 29413” was en e ed as a synonym o
T icho mus a iabilis ATCC 29413). Imp o emen s o some
bioin o ma ics ools sugges ed by he Ad iso y Boa d membe s ha e
also been inco po a ed, e.g., weha e ex ended he Sequence Pa e n
Sea ch capabili ies o he websi e so ha sea ches can bepe o med
no jus agains he genome and p o eome o a single o ganism bu
agains a se o pep ides lis ed in a Sma Table, o agains he ull
p o eomes o mul iple o ganisms lis ed in a Sma Table such as hose
in Table2.
We will con inue o de elop he CyanoCyc po al o add ess he
needs o he cyanobac e ial communi y. Fo example, wecould impo
da a on ansc ip ion s a si es, e mina o s, and ansc ip ion ac o
binding si es, i a ailable; add connec ions o o he da abases, such as
CyanoSou ce ha has a lib a y o ba coded knockou mu an s o
Synechocys is sp. PCC 6803 mu an s; o gene a e a Flux Balance
Analysis me abolic model o Synechocys is sp. PCC 6803 ha use s
can un. These u u e imp o emen s o he da abases will beexplo ed
wi h inpu om he Ad iso y Boa d and he la ge communi y.
Cyanobac e ial scien is s can con ibu e o CyanoCyc in se e al
ways. A he bo om o e e y CyanoCyc web page is a link “Repo
E o s o P o ide Feedback” which can beused o epo da a e o s
o e o s in he so wa e ools, and o submi sugges ions o imp o ed
unc ionali y. Fo hose in e es ed in making a longe e m se ies o
enhancemen s o he da abases, please con ac us h ough he abo e
link o ia email o he co esponding au ho . We will p o ide
youwi h access o ou web-based da abase edi ing ools ha cu a o s
use o make upda es o he da abases.
Wha can youdo wi h CyanoCyc?
He e we explo e some o he ope a ions he CyanoCyc
bioin o ma ics ools p o ide, g ouped in o i e ca ego ies: genomic,
me abolic, egula o y, omics-da a analy ic, and compa a i e
ope a ions, and p o ide guidance abou how o access he ools and
gene a e he example igu es.
Genomic ope a ions include sea ching o genes and hei
p oduc s by name using he Sea ch in Cu en Da abase ield o ( ia
he ad anced sea ch Tools > Sea ch > Sea ch Genes, P o eins, o
RNAs) by addi ional p ope ies including pI and p o ein ea u es,
such as amino acid me al binding si es. The esul s a e shown as
Gene/P o ein In o ma ion pages ( o ins ance, ndbA, Figu e1). F om
he gene page, he use can e ie e he nucleo ide sequence o he
TABLE2 Sma Tables lis ing CyanoCyc o ganisms g ouped acco ding o
hei pheno ype.
Sma Table name Numbe o da abases
Cyanobac e ia Lis : Filamen ous O ganisms 127
Cyanobac e ia Lis : He e ocys Fo me s 66
Cyanobac e ia Lis : Ni ogen Fixing O ganisms 89
Cyanobac e ia Lis : Obliga e Symbion s 9
Cyanobac e ia Lis : Picocyanobac e ia 60
Cyanobac e ia Lis : Unicellula Cyanobac e ia 140
These Sma Tables, c ea ed Feb ua y 27, 2023, can be ound in he lis ing o all Public
Sma Tables. Since he i le o each able s a s wi h “Cyanobac e ia Lis ,” i is easy o sea ch
o (“Fil e ”) hem. Each Public Sma Table indica es he c i e ia used o include o exclude
speci ic cyanobac e ia da abases and p o ides ime s amps o when hey a e upda ed.
TABLE3 The numbe o Tie 3 da abases o which he o hologs we e
p opaga ed om he cu a ed da abase and he a e age numbe s o
cu a ed genes p opaga ed o o hologs in he ecipien da abases.
Cu a ed da abase Tie 3 da abases
ecei ing
o holog
in o ma ion
A e age numbe
o p opaga ed
genes pe
da abase ( ange)
Synechocys is sp. PCC 6803 6 313 (288–323)
Synechococcus elonga us
PCC 7942
4 486 (441–529)
Synechococcus sp. WH8102 4 410 (120–526)
P. m a inu s SS120 16 53 (46–64)
P. m a inu s MED4 16 18 (16–19)
Links o he cu a ed da abase a e p o ided. Da a o Synechocys is sp. PCC 6803 is om
BioCyc e sion 27.5, eleased on Decembe 8, 2023; da a o o he da abases is om BioCyc
e sion 27.1, eleased on Augus 28, 2023.

Moo e e al. 10.3389/ micb.2024.1340413
F on ie s in Mic obiology 06 on ie sin.o g
FIGURE1
Example o page desc ibing a gene, ndbA o Synechocys is sp. PCC 6803, encoding a subuni o a ype II NADH Dehyd ogenase. URL: h ps://
cyanocyc.o g/gene?o gid=GCF_000009725&id=SGL_RS08135. To gene a e his page online: (1) Open CyanoCyc.o g in a web b owse . (2) Click
bu on “Change Cu en Da abase,” hen ype “kazusa” in o he box unde “Selec a Da abase,” and click on “Synechocys is sp. PCC 6803 subs .
Kazusa” ha appea s jus benea h, hen click OK. (3) Jus below and o he igh o he “Change Cu en Da abase” is he ex en y box o sea ching
– ype “ndbA” in o ha box and p ess En e o each he page o ha gene.
Moo e e al. 10.3389/ micb.2024.1340413
F on ie s in Mic obiology 07 on ie sin.o g
coding egion, o o a use -de ined genome egion, o he amino-acid
sequence o he gene p oduc . The si e suppo s BLAST sea ches
agains all o BioCyc and agains indi idual genomes. The la e a e
qui e apid, app oxima ely 15 s. Sequence pa e n sea ches o
nucleo ide and amino-acid sequences a e also suppo ed based on
he Pa Ma ch sequence-pa e n language (Yan e al., 2005). CyanoCyc
p o ides bo h linea and ci cula genome b owse s ha enable he
use o zoom om he sequence le el o a single-page iew o an
en i e eplicon. The use can also execu e sequence alignmen s
among mul iple selec ed sequences. A pos e -size genome map
diag am can be gene a ed using Tools > Genome > Gene a e
Genome Pos e .
Me abolic ope a ions include sea ches o me aboli es,
eac ions, and me abolic pa hways using names, o by o he c i e ia
including me aboli e monoiso opic mass, chemical o mula, and
InChI s ing using ad anced sea ch ools such as Tools > Sea ch
Compounds. The esul s a e shown as in o ma ion pages o
me aboli es (e.g., cyanop e in, Figu e 2), eac ions (e.g., EC
4.1.2.13), and pa hways (e.g., echinenone and zeaxan hin
biosyn hesis and linea elec on low wi h plas ocyanin). Me abolic
pa hway diag ams a e au oma ically d awn by he so wa e wi h
use selec ion o he de ail le el ha can d ill down om key
eac an names o egula o s o me aboli e s uc u es. Th ee ools
a e p o ided o explo ing comple e me abolic ne wo ks (see Tools
> Me abolism). (1) The Cellula O e iew p o ides zoomable,
sea chable, o ganism-speci ic me abolic ne wo k diag ams o
e e y CyanoCyc o ganism (Figu e3), and a p in able pos e -size
me abolic cha diag am can begene a ed om his diag am using
Tools > Me abolism > Gene a e Me abolic Map Pos e . (2) The
Me abolic Rou e Sea ch ool enables he use o speci y s a ing
and ending me aboli es o in e es ; he ool gene a es al e na i e
minimal-cos ou es h ough he ne wo k ha connec s hese
me aboli es. (3) The Me abolic Ne wo k Explo e ool is simila o
Me abolic Rou e Sea ch bu suppo s in e ac i e, inc emen al
explo a ion: he use s a s a a me aboli e o in e es and
inc emen ally adds one eac ion a a ime, building up a use -
guided pa hway om one me aboli e o ano he .
Regula o y ope a ions consis o isualiza ion ools o a ious
egula o y ela ionships. Gene pages con ain a egula ion summa y
diag am ha depic s all he a ailable egula o y in luences on he gene
and i s p oduc , including ansc ip ional, ansla ional, and pos -
ansla ional egula ion. Gene pages o ansc ip ion ac o s con ain
a Regulon ab ha depic s all ope ons con olled by he ansc ip ion
ac o , p o ided ha in o ma ion has been cu a ed. A egula o y
ne wo k b owse ool (see Tools > Genome) depic s he ull egula o y
ne wo k o o ganisms con aining signi ican numbe s o egula o y
FIGURE2
Example o page desc ibing he me aboli e cyanop e in. URL: h ps://cyanocyc.o g/compound?o gid=GCF_000009725&id=CPD-26623. To ge o
his page: (1) Follow he ins uc ions p o ided o Figu e1, excep en e “cyanop e in” in o he Sea ch in Cu en Da abase ield and p ess En e . (2)
Se e al sea ch esul s a e shown; click “cyanop e in” unde he Compounds sec ion o go o he me aboli e page shown he e.
Moo e e al. 10.3389/ micb.2024.1340413
F on ie s in Mic obiology 08 on ie sin.o g
FIGURE3
A cellula o e iew o he cyanobac e ium Synechocys is sp. PCC 6803 (URL: h ps://biocyc.o g/o e iewsWeb/celO .sh ml?o gid=GCF_000009725)
wi h supe imposed omics da a om an expe imen s udying he e ec o excess i on on he o ganism (one ime poin om GEO da ase #
GDS3741, Houo e al., 2007). To gene a e his igu e: (1) Wi hin he Synechocys is sp. PCC 6803 subs . Kazusa PGDB, go o he Tools d op
down menu, hen selec on Cellula O e iew unde nea h he Me abolism sec ion. (2) Once on he Cellula O e iew page, click on Impo Da a
om GEO unde he OPERATIONS panel o he igh o he page. (3) In he pop-up window ha opens, en e he GEO da ase # in he
Keywo ds box and p ess Go o connec o he da ase . (4) Highligh he da a o display, such as GSM84561, and p ess Submi . (5) Change he
Colo s Scheme, Y-Axis scale and un he Anima ion using he Omics Con ol Panel ha pops up once he da a is o e laid. A low diag am o
hese ins uc ions is also a ailable in Supplemen a y Figu e S1; hese can beused as a s a ing o poin o displaying o he omics da a on he
Cellula O e iew.
in e ac ions. The numbe o egula o y in e ac ions cu a ed in he
CyanoCyc da abases is, as ye , ela i ely small.
Omics analy ic ope a ions a e a ailable o ansc ip omic,
p o eomic, and me abolomic da a.
The ools include:
• En ichmen analysis o me abolic pa hways o ansc ip omic,
p o eomics and me abolomic da a
• Visualiza ion o ansc ip omic, p o eomic, and me abolomic
da a on indi idual pa hways, on mul i-pa hway diag ams
called pa hway collages, and on a ull me abolic ne wo k
diag am o he o ganism. The la e isualiza ion can
beanima ed o da ase s con aining mul iple obse a ions.
• Visualiza ion o ansc ip omic, p o eomic, and me abolomic
da a on a sys em-o ien ed diag am called he Omics Dashboa d
(Figu e4), which depic s he ac i a ion le els o e e y subsys em
wi hin he cell and enables he use o p obe he exp ession le els
o indi idual subsys ems in mo e de ail.
Compa a i e ope a ions include se e al ools ha le e age
he o holog in o ma ion in CyanoCyc. The genome b owse has
a compa a i e mode ha enables he use o align eplicons om
mul iple o ganisms a an o hologous gene g oup o compa e he
genome con ex a ound hose genes (Figu e5). This has been
used o de e mine he ex en o conse a ion in genome s uc u e
o cy och ome c6 genes (To ado e al., 2023) and c E genes
(Sa a e  al., 2022) in di e se cyanobac e ia. A ela ed ool
p oduces a able lis ing o a g oup o o hologous genes including
he gene name, anno a ed unc ion, and a diag am o he
con aining ope on.
Moo e e al. 10.3389/ micb.2024.1340413
F on ie s in Mic obiology 09 on ie sin.o g
A sui e o compa a i e analysis ools (Tools > Analysis >
Compa a i e Analysis) gene a es ables compa ing s a is ics
ac oss a selec ed se o genomes, anging om compa isons o
p o eomes (e.g., iden i ying p o eins ha ha e no o hologs in he
o he o ganisms), pa hways, eac ions, me aboli es,
and anspo e s.
FIGURE4
The Omics Dashboa d da a analysis ool showing ansc ip ion le els o Synechocys is sp. PCC 6803 genes in ol ed in amino acid biosyn hesis om a
cul u e g own wi h a low amoun o sul u (GEO da ase # GDS3745, Zhang e al., 2008). To gene a e his igu e: (1) Follow ins uc ions o Figu e3 excep
use he GEO da ase # GDS3745 and highligh ep1 o ime poin s 1–72  h unde sul a e dep i a ion; p ess Submi . (2) Selec “Expo o Dashboa d” a he
bo om o he Omics Con ol Panel o open he da a in a new b owse window. (3) In he Biosyn hesis da a panel, mouse o e he da a a ea o AA Syn
and click o open a new window showing he a e age gene exp ession da a o he enzymes in ol ed in biosyn hesis o each amino acid.
FIGURE5
A compa a i e genome b owse showing glyA gene o hologs ac oss i e cyanobac e ial species and he genome con ex a ound he glyA o hologs
using he “Align in Mul i-Genome B owse ” ool. URL: h ps://cyanocyc.o g/genb o/o ho.sh ml?lead-o gid=GCF_000009725&lead-genes=SGL_RS04
690&o gids=GCF_000010625,SS120,SYNEL,GCF_000009725,GCF_000204075. To make his igu e: (1) Wi h he Synechocys is sp. PCC 6803 subs .
Kazusa PGDB selec ed as he cu en da abase, en e he s ing “glyA” in o he “Sea ch in Cu en Da abase” ield and p ess En e . (2) Choose “Align in
Mul i-Genome B owse ” unde he Ope a ions panel on he igh -hand side o he gene/p o ein in o ma ion page. (3) A window opens allowing he
use o “Speci y Lis o O ganism Da abases” o beused in he alignmen . (4) On he le -hand side, en e he name o o ganism desi ed, e.g.,
Mic ocys is ae uginosa NIES-843, in he ield, highligh (i necessa y), hen click “Add →” o pu i in o he Cu en Selec ion lis on he igh -hand side.
(5). When you lis is comple e, push he “OK” bu on a he bo om igh o gene a e he igu e.