Re-annotating the Mycoplasma pneumoniae genome sequence: Adding value, function and reading frames

Thomas Dandekar, Martijn Huynen, Jörg Thomas Regula, Barbara Ueberle, Carl Ulrich Zimmermann, Miguel A. Andrade, Tobias Doerks, Luis Sánchez-Pulido, Berend Snel, Mikita Suyama, Yan P. Yuan, Richard Herrmann, Peer Bork

Research output: Contribution to journalArticle

184 Citations (Scopus)

Abstract

Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from 39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified. Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent annotation vocabulary has been introduced. Annotation reasoning, annotation categories and comparisons to other published data on M.pneumoniae functional assignments are given. Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins with predicted functional features from 349 to 458. The increase includes 36 new predictions and 73 protein assignments confirmed by the published literature. Furthermore, there are 23 reductions and 30 additions with respect to the previous annotation. mRNA expression data support transcription of 184 of the functionally unassigned reading frames.

Original languageEnglish
Pages (from-to)3278-3288
Number of pages11
JournalNucleic Acids Research
Volume28
Issue number17
Publication statusPublished - Sep 1 2000
Externally publishedYes

Fingerprint

Reading Frames
Mycoplasma pneumoniae
Genome
Open Reading Frames
RNA
Proteins
Mass Spectrometry
RNA, Transfer, Leu
Intergenic DNA
Vocabulary
Transfer RNA
Electrophoresis
Pneumonia
Gels
Gene Expression
Messenger RNA
Genes

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Dandekar, T., Huynen, M., Regula, J. T., Ueberle, B., Zimmermann, C. U., Andrade, M. A., ... Bork, P. (2000). Re-annotating the Mycoplasma pneumoniae genome sequence: Adding value, function and reading frames. Nucleic Acids Research, 28(17), 3278-3288.

Re-annotating the Mycoplasma pneumoniae genome sequence : Adding value, function and reading frames. / Dandekar, Thomas; Huynen, Martijn; Regula, Jörg Thomas; Ueberle, Barbara; Zimmermann, Carl Ulrich; Andrade, Miguel A.; Doerks, Tobias; Sánchez-Pulido, Luis; Snel, Berend; Suyama, Mikita; Yuan, Yan P.; Herrmann, Richard; Bork, Peer.

In: Nucleic Acids Research, Vol. 28, No. 17, 01.09.2000, p. 3278-3288.

Research output: Contribution to journalArticle

Dandekar, T, Huynen, M, Regula, JT, Ueberle, B, Zimmermann, CU, Andrade, MA, Doerks, T, Sánchez-Pulido, L, Snel, B, Suyama, M, Yuan, YP, Herrmann, R & Bork, P 2000, 'Re-annotating the Mycoplasma pneumoniae genome sequence: Adding value, function and reading frames', Nucleic Acids Research, vol. 28, no. 17, pp. 3278-3288.
Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA et al. Re-annotating the Mycoplasma pneumoniae genome sequence: Adding value, function and reading frames. Nucleic Acids Research. 2000 Sep 1;28(17):3278-3288.
Dandekar, Thomas ; Huynen, Martijn ; Regula, Jörg Thomas ; Ueberle, Barbara ; Zimmermann, Carl Ulrich ; Andrade, Miguel A. ; Doerks, Tobias ; Sánchez-Pulido, Luis ; Snel, Berend ; Suyama, Mikita ; Yuan, Yan P. ; Herrmann, Richard ; Bork, Peer. / Re-annotating the Mycoplasma pneumoniae genome sequence : Adding value, function and reading frames. In: Nucleic Acids Research. 2000 ; Vol. 28, No. 17. pp. 3278-3288.
@article{ab533525962044a18b1e58326dba5ce5,
title = "Re-annotating the Mycoplasma pneumoniae genome sequence: Adding value, function and reading frames",
abstract = "Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from 39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified. Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent annotation vocabulary has been introduced. Annotation reasoning, annotation categories and comparisons to other published data on M.pneumoniae functional assignments are given. Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins with predicted functional features from 349 to 458. The increase includes 36 new predictions and 73 protein assignments confirmed by the published literature. Furthermore, there are 23 reductions and 30 additions with respect to the previous annotation. mRNA expression data support transcription of 184 of the functionally unassigned reading frames.",
author = "Thomas Dandekar and Martijn Huynen and Regula, {J{\"o}rg Thomas} and Barbara Ueberle and Zimmermann, {Carl Ulrich} and Andrade, {Miguel A.} and Tobias Doerks and Luis S{\'a}nchez-Pulido and Berend Snel and Mikita Suyama and Yuan, {Yan P.} and Richard Herrmann and Peer Bork",
year = "2000",
month = "9",
day = "1",
language = "English",
volume = "28",
pages = "3278--3288",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "17",

}

TY - JOUR

T1 - Re-annotating the Mycoplasma pneumoniae genome sequence

T2 - Adding value, function and reading frames

AU - Dandekar, Thomas

AU - Huynen, Martijn

AU - Regula, Jörg Thomas

AU - Ueberle, Barbara

AU - Zimmermann, Carl Ulrich

AU - Andrade, Miguel A.

AU - Doerks, Tobias

AU - Sánchez-Pulido, Luis

AU - Snel, Berend

AU - Suyama, Mikita

AU - Yuan, Yan P.

AU - Herrmann, Richard

AU - Bork, Peer

PY - 2000/9/1

Y1 - 2000/9/1

N2 - Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from 39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified. Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent annotation vocabulary has been introduced. Annotation reasoning, annotation categories and comparisons to other published data on M.pneumoniae functional assignments are given. Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins with predicted functional features from 349 to 458. The increase includes 36 new predictions and 73 protein assignments confirmed by the published literature. Furthermore, there are 23 reductions and 30 additions with respect to the previous annotation. mRNA expression data support transcription of 184 of the functionally unassigned reading frames.

AB - Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from 39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified. Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent annotation vocabulary has been introduced. Annotation reasoning, annotation categories and comparisons to other published data on M.pneumoniae functional assignments are given. Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins with predicted functional features from 349 to 458. The increase includes 36 new predictions and 73 protein assignments confirmed by the published literature. Furthermore, there are 23 reductions and 30 additions with respect to the previous annotation. mRNA expression data support transcription of 184 of the functionally unassigned reading frames.

UR - http://www.scopus.com/inward/record.url?scp=0034284160&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0034284160&partnerID=8YFLogxK

M3 - Article

C2 - 10954595

AN - SCOPUS:0034284160

VL - 28

SP - 3278

EP - 3288

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 17

ER -