Letter to the Editor on ‘The urgency of annotating pathogen hypothetical genes’

Gene Reports

Volumn 4, Issue , 2016, Pages 233-234

  Patel, Seema ^a  

^a SAN DIEGO STATE UNIVERSITY   (United States)

Author keywords

Annotation; Hypothetical genes; In vitro adaptation

Indexed keywords

BACTERIAL ENZYME; BACTERIAL PROTEIN; TRANSCRIPTION FACTOR;

BACTERIAL GENE; BACTERIAL GENOME; EVOLUTIONARY ADAPTATION; GENOME ANALYSIS; IN VITRO STUDY; LETTER; MOLECULAR GENETICS; NONHUMAN; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

EID: 84978215731     PISSN: 24520144     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.genrep.2016.07.004     Document Type: Letter

References (16)

1. Aujoulat, F., Roger, F., Bourdier, A., Lotthé, A., Lamy, B., Marchandin, H., Jumas-Bilak, E., From environment to man: genome evolution and adaptation of human opportunistic bacterial pathogens. Genes (Basel) 3 (2012), 191–232, 10.3390/genes3020191.
2. Basu, S., Bose, C., Ojha, N., Das, N., Das, J., Pal, M., Khurana, S., Evolution of bacterial and fungal growth media. Bioinformation 11 (2015), 182–184, 10.6026/97320630011182.
3. Berg, J.M., Tymoczko, J.L., Stryer, L., Enzymes are Powerful and Highly Specific Catalysts. 2002.
4. Bielaszewska, M., Prager, R., Köck, R., Mellmann, A., Zhang, W., Tschäpe, H., Tarr, P.I., Karch, H., Shiga toxin gene loss and transfer in vitro and in vivo during enterohemorrhagic Escherichia coli O26 infection in humans. Appl. Environ. Microbiol. 73 (2007), 3144–3150, 10.1128/AEM.02937-06.
5. Darmon, E., Leach, D.R.F., Bacterial genome instability. Microbiol. Mol. Biol. Rev. 78 (2014), 1–39, 10.1128/MMBR.00035-13.
6. Domenech, P., Rog, A., Moolji, J., Radomski, N., Fallow, A., Leon-Solis, L., Bowes, J., Behr, M.A., Reed, M.B., Origins of a 350-kilobase genomic duplication in Mycobacterium tuberculosis and its impact on virulence. Infect. Immun. 82 (2014), 2902–2912, 10.1128/IAI.01791-14.
7. Esko, J.D., Sharon, N., Microbial Lectins: Hemagglutinins, Adhesins, and Toxins. 2009.
8. Gil, R., Latorre, A., Factors behind junk DNA in bacteria. Genes (Basel) 3 (2012), 634–650, 10.3390/genes3040634.
9. Gillespie, J.J., Wattam, A.R., Cammer, S.A., Gabbard, J.L., Shukla, M.P., Dalay, O., Driscoll, T., Hix, D., Mane, S.P., Mao, C., Nordberg, E.K., Scott, M., Schulman, J.R., Snyder, E.E., Sullivan, D.E., Wang, C., Warren, A., Williams, K.P., Xue, T., Yoo, H.S., Zhang, C., Zhang, Y., Will, R., Kenyon, R.W., Sobral, B.W., PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect. Immun. 79 (2011), 4286–4298, 10.1128/IAI.00207-11.
10. Losada, L., Ronning, C.M., DeShazer, D., Woods, D., Fedorova, N., Kim, H.S., Shabalina, S.A., Pearson, T.R., Brinkac, L., Tan, P., Nandi, T., Crabtree, J., Badger, J., Beckstrom-Sternberg, S., Saqib, M., Schutzer, S.E., Keim, P., Nierman, W.C., Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biol. Evol. 2 (2010), 102–116, 10.1093/gbe/evq003.
11. Mazandu, G.K., Mulder, N.J., Function prediction and analysis of Mycobacterium tuberculosis hypothetical proteins. Int. J. Mol. Sci. 13 (2012), 7283–7302, 10.3390/ijms13067283.
12. Ortega, C., Anderson, L.N., Frando, A., Sadler, N.C., Brown, R.W., Smith, R.D., Wright, A.T., Grundner, C., Systematic survey of serine hydrolase activity in Mycobacterium tuberculosis defines changes associated with persistence. Cell Chem. Biol. 23 (2016), 290–298, 10.1016/j.chembiol.2016.01.003.
13. Sellek, R.E., Escudero, R., Gil, H., Rodríguez, I., Chaparro, E., Pérez-Pastrana, E., Vivo, A., Anda, P., In vitro culture of Borrelia garinii results in loss of flagella and decreased invasiveness. Infect. Immun. 70 (2002), 4851–4858.
14. Shitikov, E.A., Bespyatykh, J.A., Ischenko, D.S., Alexeev, D.G., Karpova, I.Y., Kostryukova, E.S., Isaeva, Y.D., Nosova, E.Y., Mokrousov, I.V., Vyazovaya, A.A., Narvskaya, O.V., Vishnevsky, B.I., Otten, T.F., Zhuravlev, V.I., Zhuravlev, V.Y., Yablonsky, P.K., Ilina, E.N., Govorun, V.M., Unusual large-scale chromosomal rearrangements in Mycobacterium tuberculosis Beijing B0/W148 cluster isolates. PLoS One, 9, 2014, e84971, 10.1371/journal.pone.0084971.
15. Sivashankari, S., Shanmughavel, P., Functional annotation of hypothetical proteins - a review. Bioinformation 1 (2006), 335–338.
16. Somerville, G.A., Beres, S.B., Fitzgerald, J.R., DeLeo, F.R., Cole, R.L., Hoff, J.S., Musser, J.M., In vitro serial passage of Staphylococcus aureus: changes in physiology, virulence factor production, and agr nucleotide sequence. J. Bacteriol. 184 (2002), 1430–1437.