First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1

Prasse, Daniela; Thomsen, Jakob Borup; Santis, Rebecca De; Muntel, Jan; Becher, Dörte; Schmitz, Ruth A.

doi:10.1016/j.biochi.2015.04.007

Cited by 29 publications

(34 citation statements)

References 98 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, recent findings that prokaryotes in general have high fractions of translated leaderless mRNAs [18,19] and sORFs (small open reading frames) [20,21] make the realization of intraRNAs coding potential worth investigating. Pervasive translation of intraRNAs would include prokaryotes into the meaningfulness of protein isoforms debate [22,23].…”

Section: Introductionmentioning

confidence: 99%

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

View full text Add to dashboard Cite

Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.

show abstract

Section: Introductionmentioning

confidence: 99%

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

View full text Add to dashboard Cite

show abstract

“…In archaea a few small proteins have been reported, the majority of which is regulated in response to a specific stress. However, for most of them verified functional analysis is scarce or missing (Prasse et al (2015), Cassidy et al (2016), Cassidy et al (2018), Nagel et al (2019), Kubatova et al (2019), Jevtic et al (2019 Methanosarcina mazei strain Gö1 belongs to the methylotrophic methanogens of the order Methanosarcinales, which have the most versatile substrate spectrum within the methanogenic archaea and significantly contribute to the production of the greenhouse gas (Ferry (1999)). M. mazei is able to fix molecular nitrogen under nitrogen limitation.…”

Section: Introductionmentioning

confidence: 99%

“…Besides, RNAseq and term-seq approaches not only identified high numbers of small non-coding RNAs but also numerous small mRNAs in M. mazei containing putative sORFs (Dar et al (2016), Jager et al (2009 as well as unpublished RNAseq data sets). Aiming to elucidate whether the predicted sORFs identified are translated in vivo, the full cytosolic proteome of M. mazei was examined using reversed phase LC-MS MS approaches (bottom up and top down strategies) as described in Prasse et al (2015), Cassidy et al (2019), Cassidy et al (2016)). In these comprehensive studies overall 40 small proteins were detected and experimentally validated with high or mid confidence (Cassidy et al (2019), Cassidy et al (2016)).…”

Section: Introductionmentioning

confidence: 99%

Small protein 26 interacts and enhances glutamine synthetase activity inMethanosarcina mazei

Gutt

Jordan

Weidenbach

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Small ORFs (sORF) encoded small proteins have been overlooked for a long time due to challenges in prediction and distinguishing between coding and non-coding predicted sORFs and in their biochemical detection and characterization. We report on the first biochemical and functional characterization of a small protein (sP26) in the archaeal model organism Methanosarcina mazei, comprising 23 amino acids. The corresponding encoding leaderless mRNA (spRNA26) is highly conserved within numerous Methanosarcina strains on the amino acid as well as on nucleotide level strongly arguing for a cellular function of the small protein. spRNA26 is significantly enhanced under nitrogen limitation, but also under oxygen and salt stress conditions. His-tagged sP26 was heterologously expressed and purified by fractionated ammonium sulfate precipitation, affinity chromatography and size exclusion centrifugation. Using independent biochemical approaches (pull-down by affinity chromatography followed by MS analysis, revers pull-down, microscale thermophoresis and size exclusion chromatography) we observed that sP26 interacts and forms complexes with M. mazei glutamine synthetase (GlnA 1 ) with high affinity (app. KD = 45 +/-14 µM). Upon interaction with sP26, GlnA 1 activity was significantly stimulated independently and in addition to the known activation by the metabolite 2-oxoglutarate. Besides strong interaction of sP26 with the PII-like protein GlnK 1 was demonstrated (KD= 1.4 µM +/-0.9 µM). On the basis of these findings, we hypothesize that in addition to 2-oxoglutarate, sP26activates GlnA 1 activity under nitrogen limitation most likely by stabilizing the dodecameric structure of GlnA 1 .

show abstract

“…The presence and function of small proteins in the third domain of life, archaea, are currently understudied. Analyses of small proteins in archaea have only recently been published . In these studies, small proteins encoded by previously identified sRNAs were found to be expressed in Methanosarcina mazei .…”

Section: Introductionmentioning

confidence: 99%

“…Analyses of small proteins in archaea have only recently been published . In these studies, small proteins encoded by previously identified sRNAs were found to be expressed in Methanosarcina mazei . Their expression pattern suggests that one of them might be involved in nitrogen regulation, but the function of these small proteins is not known yet.…”

Section: Introductionmentioning

confidence: 99%

Solution Structure and Dynamics of the Small Protein HVO_2922 from Haloferax volcanii

et al. 2019

View full text Add to dashboard Cite

Past sequencing campaigns overlooked small proteins as they seemed to be irrelevant due to their small size. However, their occurrence is widespread, and there is growing evidence that these small proteins are in fact functionally very important in organisms found in all kingdoms of life. Within a global proteome analysis for small proteins of the archaeal model organism Haloferax volcanii, the HVO_2922 protein has been identified. It is differentially expressed in response to changes in iron and salt concentrations, thus suggesting that its expression is stress‐regulated. The protein is conserved among Haloarchaea and contains an uncharacterized domain of unknown function (DUF1508, UPF0339 family protein). We elucidated the NMR solution structure, which shows that the isolated protein forms a symmetrical dimer. The dimerization is found to be concentration‐dependent and essential for protein stability and most likely for its functionality, as mutagenesis at the dimer interface leads to a decrease in stability and protein aggregation.

show abstract

First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1

Cited by 29 publications

References 98 publications

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Small protein 26 interacts and enhances glutamine synthetase activity inMethanosarcina mazei

Solution Structure and Dynamics of the Small Protein HVO_2922 from Haloferax volcanii

Contact Info

Product

Resources

About