Optimization of RNA isolation from the archaebacterium Methanosarcina barkeri and validation for oligonucleotide microarray analysis

Physiological and transcriptomic response to methyl-coenzyme M reductase limitation in Methanosarcina acetivorans

Methyl-coenzyme M reductase (MCR) catalyzes the final step of methanogenesis, the microbial metabolism responsible for nearly all biological methane emissions to the atmosphere. Decades of biochemical and structural research studies have generated detailed insights into MCR function in vitro, yet very little is known about the interplay between MCR and methanogen physiology. For instance, while it is routinely stated that MCR catalyzes the rate-limiting step of methanogenesis, this has not been categorically tested. In this study, to gain a more direct understanding of MCR's control on the growth of Methanosarcina acetivorans, we generate a strain with an inducible mcr operon on the chromosome, allowing for careful control of MCR expression. We show that MCR is not growth rate-limiting in substrate-replete batch cultures. However, through careful titration of MCR expression, growth-limiting state(s) can be obtained. Transcriptomic analysis of M. acetivorans experiencing MCR limitation reveals a global response with hundreds of differentially expressed genes across diverse functional categories. Notably, MCR limitation leads to strong induction of methylsulfide methyltransferases, likely due to insufficient recycling of metabolic intermediates. In addition, the mcr operon is not transcriptionally regulated, i.e., it is constitutively expressed, suggesting that the overabundance of MCR might be beneficial when cells experience nutrient limitation or stressful conditions. Altogether, we show that there is a wide range of cellular MCR concentrations that can sustain optimal growth, suggesting that other factors such as anabolic reactions might be rate-limiting for methanogenic growth.

IMPORTANCE

Methane is a potent greenhouse gas that has contributed to ca. 25% of global warming in the post-industrial era. Atmospheric methane is primarily of biogenic origin, mostly produced by microorganisms called methanogens. Methyl-coenzyme M reductase (MCR) catalyzes methane formatio in methanogens. Even though MCR comprises ca. 10% of the cellular proteome, it is hypothesized to be growth-limiting during methanogenesis. In this study, we show that Methanosarcina acetivorans cells grown in substrate-replicate batch cultures produce more MCR than its cellular demand for optimal growth. The tools outlined in this study can be used to refine metabolic models of methanogenesis and assay lesions in MCR in a higher-throughput manner than isolation and biochemical characterization of pure protein.

Clinical significance of decreased programmed cell death 4 expression in patients with giant cell tumors of the bone

Programmed cell death 4 (PDCD4) has been recognized as a novel tumor suppressor gene, which inhibits the activation and translation of activator protein (AP)-1. Dysregulated expression of PDCD4 is also involved in various human tumors and is linked to tumor progression and development. However, the function and clinical implication of PDCD4 in giant cell tumors of the bone (GCTBs) has not been previously investigated. In the present study, PDCD4 expression was determined in 83 samples of GCTBs at mRNA and protein levels by quantitative reverse transcription-polymerase chain reaction, western blotting and immunohistochemistry. The results demonstrated that PDCD4 mRNA expression was reduced in 63% of GCTB samples (17/27) and protein expression was decreased in 65% of samples (54/83), compared with adjacent non-tumor tissues. Furthermore, decreased expression of PDCD4 was significantly associated with certain clinicopathological characteristics, including the Campanacci grade and recurrence. A strong negative correlation was determined between PDCD4 expression and the Ki-67 positive rate in GCTBs (r=−0.6392; P<0.001). The results of the present study suggest that PDCD4 may serve a role in the malignant progression of human GCTBs and may be an important prediction factor for prognosis.

Response of a rice paddy soil methanogen to syntrophic growth as revealed by transcriptional analyses

Members of Methanocellales are widespread in paddy field soils and play the key role in methane production. These methanogens feature largely in these organisms’ adaptation to low H2 and syntrophic growth with anaerobic fatty acid oxidizers. The adaptive mechanisms, however, remain unknown. In the present study, we determined the transcripts of 21 genes involved in the key steps of methanogenesis and acetate assimilation of Methanocella conradii HZ254, a strain recently isolated from paddy field soil. M. conradii was grown in monoculture and syntrophically with Pelotomaculum thermopropionicum (a propionate syntroph) or Syntrophothermus lipocalidus (a butyrate syntroph). Comparison of the relative transcript abundances showed that three hydrogenase-encoding genes and all methanogenesis-related genes tested were upregulated in cocultures relative to monoculture. The genes encoding formylmethanofuran dehydrogenase (Fwd), heterodisulfide reductase (Hdr), and the membrane-bound energy-converting hydrogenase (Ech) were the most upregulated among the evaluated genes. The expression of the formate dehydrogenase (Fdh)-encoding gene also was significantly upregulated. In contrast, an acetate assimilation gene was downregulated in cocultures. The genes coding for Fwd, Hdr, and the D subunit of F420-nonreducing hydrogenase (Mvh) form a large predicted transcription unit; therefore, the Mvh/Hdr/Fwd complex, capable of mediating the electron bifurcation and connecting the first and last steps of methanogenesis, was predicted to be formed in M. conradii. We propose that Methanocella methanogens cope with low H2 and syntrophic growth by (i) stabilizing the Mvh/Hdr/Fwd complex and (ii) activating formatedependent methanogenesis.

Measurement of microbial adhesive forces with a parallel plate flow chamber

HYPOTHESIS

It was predicted that the colloidal behaviors of archaea and bacteria with disparate surface structure were different. In this study, the effects of the physicochemical properties of microbial cell surfaces on colloidal behavior were analyzed with Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, thermodynamics, and powder technology.

EXPERIMENTS

Cell attachment and detachment from model substrates were directly observed using a parallel plate flow chamber. Gram-negative Escherichia coli and archaeal Methanosarcina barkeri were used as model microbial cells, and positively and negatively charged glass slides were used as model substrates.

FINDINGS

Microbial adhesion on both substrates agreed well with predictions calculated from DLVO theory, using experimental parameters. The total number of cells detached from the substrates as a function of flow rate was fit with the Weibull distribution function. In addition, the drag force required for detachment, which was estimated from the hydrodynamic forces, had a wide distribution; however, the forces became smaller with increasing ionic strength because of reduced electrostatic interactions between the cells and the substrate. M. barkeri could not be detached from positively charged substrates because it would entail a negative change in the interfacial energy of interaction. Thus adhesion was thermodynamically favored in this case.

Rapid extraction of total RNA from an anaerobic sludge biocoenosis

In order to assess the activity of metabolic pathways during anaerobic biogas production, it is necessary to isolate total RNA from the anaerobic sludge. mRNA activity profiling complements the quantification of excreted metabolites for a comprehensive anaerobic digestion model (ADM1). Four non-commercial total RNA extraction protocols were examined to extract total RNA from suspended solids of anaerobic sludge. The most suitable protocol was identified and optimised. In relation to total RNA extraction efficiency, total RNA purity and RNA integrity, the best homogenisation method was a combined method of nitrogen grinding and bead beating. When bead beating or nitrogen grinding was used alone for homogenisation, total RNA extraction efficiency was lower than when both homogenisation methods were applied. Depending on the homogenisation method, the whole RNA extraction procedure takes approximately 2 to 3 h, which is as fast as when using commercial available soil RNA extraction kits. The proposed method is rapid in extracting total RNA from a biocoenosis present in an anaerobic sludge environment. Furthermore, we could apply any of the extracted homogenization methods for reverse transcription and subsequent PCR amplification of the gene for the methyl coenzyme M reductase alpha subunit (mcrA/mrtA).

Temporal and spatial coexistence of archaeal and bacterial amoA genes and gene transcripts in Lake Lucerne

Despite their crucial role in the nitrogen cycle, freshwater ecosystems are relatively rarely studied for active ammonia oxidizers (AO). This study of Lake Lucerne determined the abundance of both amoA genes and gene transcripts of ammonia-oxidizing archaea (AOA) and bacteria (AOB) over a period of 16 months, shedding more light on the role of both AO in a deep, alpine lake environment. At the surface, at 42 m water depth, and in the water layer immediately above the sediment, AOA generally outnumbered AOB. However, in the surface water during summer stratification, when both AO were low in abundance, AOB were more numerous than AOA. Temporal distribution patterns of AOA and AOB were comparable. Higher abundances of amoA gene transcripts were observed at the onset and end of summer stratification. In summer, archaeal amoA genes and transcripts correlated negatively with temperature and conductivity. Concentrations of ammonium and oxygen did not vary enough to explain the amoA gene and transcript dynamics. The observed herbivorous zooplankton may have caused a hidden flux of mineralized ammonium and a change in abundance of genes and transcripts. At the surface, AO might have been repressed during summer stratification due to nutrient limitation caused by active phytoplankton.

Contribution of transcriptomics to systems-level understanding of methanogenic Archaea

Methane-producing Archaea are of interest due to their contribution to atmospheric change and for their roles in technological applications including waste treatment and biofuel production. Although restricted to anaerobic environments, methanogens are found in a wide variety of habitats, where they commonly live in syntrophic relationships with bacterial partners. Owing to tight thermodynamic constraints of methanogenesis alone or in syntrophic metabolism, methanogens must carefully regulate their catabolic pathways including the regulation of RNA transcripts. The transcriptome is a dynamic and important control point in microbial systems. This paper assesses the impact of mRNA (transcriptome) studies on the understanding of methanogenesis with special consideration given to how methanogenesis is regulated to cope with nutrient limitation, environmental variability, and interactions with syntrophic partners. In comparison with traditional microarray-based transcriptome analyses, next-generation high-throughput RNA sequencing is greatly advantageous in assessing transcription start sites, the extent of 5′ untranslated regions, operonic structure, and the presence of small RNAs. We are still in the early stages of understanding RNA regulation but it is already clear that determinants beyond transcript abundance are highly relevant to the lifestyles of methanogens, requiring further study.

Clinical significance of programmed cell death 4 expression in malignant progression of human nasal inverted papillomas

Programmed cell death 4 (PDCD4) is a novel tumor suppressor gene that can inhibit tumor neoplastic transformation and progression in cultured cells and gene knock-out mouse models. Lost or decreased PDCD4 expression has been associated with progression and prognosis of multiple types of human tumors. However, the expression and clinical significance of PDCD4 in nasal inverted papillomas (NIPs) has not been investigated. We compared PDCD4 expression in 64 samples of NIPs, 23 of associated squamous cell carcinomas (SCCs), and 19 normal nasal samples at mRNA and protein levels by RT-PCR, western blot analysis, and immunohistochemistry. PDCD4 mRNA expression was reduced in 52% of NIP frozen samples (13/25), and the protein level was diminished in 56.3% of samples (36/64) as compared with 19 normal nasal samples, which expressed high levels of PDCD4 mRNA and protein. Furthermore, altered expression of PDCD4 was associated with the clinicopathological features Krouse stage and dysplasia. Importantly, we found a strong negative correlation of PDCD4 expression and Ki-67 labeling index in NIPs (r=-0.6645, p<0.001). In addition, the 3 tissue-sample groups significantly differed in PDCD4 expression and Ki-67 labeling index. Thus, PDCD4 expression may play a key role in pre-cancerous lesions of human NIPs and may help predict malignant progression from benign nasal tumors to associated SCC.

Reduced CMTM5 expression correlates with carcinogenesis in human epithelial ovarian cancer

OBJECTIVE

Although human chemokinelike factor (CKLF)-like MAL and related proteins for vesicle trafficking transmembrane, domain-containing member 5 (CMTM5) has been proved to play an important role in carcinogenesis and apoptosis in several types of human tumors, the expression of CMTM5 in ovarian cancer remains unclear. We aimed to investigate the association between CMTM5 expression and the survival of patients with epithelial ovarian cancer.

METHODS

Normal surface ovarian epithelium tissues, ovarian cystadenoma tissues, ovarian cancer tissues, and 5 ovarian cancer cell lines were collected. The CMTM5 expressions were determined by reverse transcription polymerase chain reaction, Western blotting, and immunohistochemical staining. The survival information was analyzed by the Kaplan-Meier method.

RESULTS

The CMTM5 expression was down-regulated in ovarian cancers. The expression of CMTM5 was absent in 30% (24 of 80) of ovarian cancers compared with 4.55% (1 of 22) of normal surface ovarian epithelium tissues and ovarian cystadenomas by immunohistochemistry. The results from the reverse transcription polymerase chain reaction were consistent with those from Western blotting. Furthermore, we found that although CMTM5 expression has no significant correlation with the age of the patients (P = 0.342), clinical stages (P = 0.155), pathologic types (P = 0.0605), or status of metastasis (P = 0.554), it was associated with the 3 groups of different differentiation levels (P = 0.0026) and an increase of CMTM5 loss of expression ratio in patients with preoperative CA125 level more than 500 mIU/mL compared to those with less than 500 mIU/mL (48.57% vs 16.67%, P = 0.0130). Statistical analysis by the Kaplan-Meier method showed that CMTM5 expression had no significant impact on the prognosis of patients with ovarian cancer (P = 0.24).

CONCLUSIONS

The reduced expression of CMTM5 correlates significantly with poorly differentiated ovarian cancer and high preoperative CA125 level. CMTM5 may contribute to the pathogenesis of human epithelial ovarian cancer.

An essential role of PDCD4 in progression and malignant proliferation of gastrointestinal stromal tumors

Programmed cell death 4 (PDCD4) is a tumor suppressor that can inhibit tumorigenesis by suppressing activator protein (AP)-1 activation and protein translation. Lost or decreased PDCD4 expression has been found in multiple types of human cancers, which was also associated with progression and metastasis of the tumors. However, the status and significance of PDCD4 in gastrointestinal stromal tumors have not been evaluated. In the present study, we examined the PDCD4 expression in a total of 63 gastrointestinal stromal tumor samples at both mRNA and protein levels by RT-PCR, western blot, and immunohistochemistry. We demonstrated that the expression of PDCD4 mRNA was diminished in 68% (17/25) of the tumor samples, and the level of PDCD4 protein appeared to be decreased in 66.7% (42/63) of the samples, as compared to adjacent normal gastrointestinal tissues, which expressed high levels of PDCD4 mRNA and protein. In addition, altered expression of PDCD4 was associated with clinicopathological parameters including risk group, tumor size, and mitosis. Moreover, PDCD4 expression had a negative correlation with the Ki-67 labeling index (r = -0.6059, P < 0.0001). All these results suggest that downregulation of PDCD4 expression may have an essential role in the progression and malignant proliferation of human gastrointestinal stromal tumors.

PDCD4 gene silencing in gliomas is associated with 5'CpG island methylation and unfavourable prognosis

Programmed cell death 4 (PDCD4) is a newly described tumour suppressor that inhibits oncogenesis by suppressing gene transcription and translation. Loss of PDCD4 expression has been found in several types of human cancers including the most common cancer of the brain, the gliomas. However, the molecular mechanisms responsible for PDCD4 gene silencing in tumour cells remain unclear. Here we report the identification of 5′CpG island methylation as the predominant cause of PDCD4 mRNA silencing in gliomas. The methylation of the PDCD4 5′CpG island was found in 47% (14/30) of glioma tissues, which was significantly associated with the loss of PDCD4 mRNA expression (γ=−1.000, P < 0.0001). Blocking methylation in glioma cells using a DNA methyltransferase inhibitor, 5-aza-2′-deoxycytidine, restored the PDCD4 gene expression, inhibited their proliferation and reduced their colony formation capacity. Longitudinal studies of a cohort of 84 patients with gliomas revealed that poor prognosis of patients with high-grade tumours were significantly associated with loss of PDCD4 expression. Thus, our current study suggests, for the first time, that PDCD4 5′CpG island methylation blocks PDCD4 expression at mRNA levels in gliomas. These results also indicate that PDCD4 reactivation might be an effective new strategy for the treatment of gliomas.

Reliable gene expression measurements from fine needle aspirates of pancreatic tumors: effect of amplicon length and quality assessment

BACKGROUND AND AIMS

Biomarker use for pancreatic cancer diagnosis has been impaired by a lack of samples suitable for reliable quantitative RT-PCR (qRT-PCR). Fine needle aspirates (FNAs) from pancreatic masses were studied to define potential causes of RNA degradation and develop methods for accurately measuring gene expression.

METHODS

Samples from 32 patients were studied. RNA degradation was assessed by using a multiplex PCR assay for varying lengths of glyceraldehyde-3-phosphate dehydrogenase, and effects on qRT-PCR were determined by using a 150-bp and a 80-bp amplicon for RPS6. Potential causes of and methods to circumvent RNA degradation were studied by using FNAs from a pancreatic cancer xenograft.

RESULTS

RNA extracted from pancreatic mass FNAs was extensively degraded. Fragmentation was related to needle bore diameter and could not be overcome by alterations in aspiration technique. Multiplex PCR for glyceraldehyde-3-phosphate dehydrogenase could distinguish samples that were suitable for qRT-PCR. The use of short PCR amplicons (<100 bp) provided reliable gene expression analysis from FNAs. When appropriate samples were used, the assay was highly reproducible for gene copy number with minimal (0.0003 or about 0.7% of total) variance.

CONCLUSIONS

The degraded properties of endoscopic FNAs markedly affect the accuracy of gene expression measurements. Our novel approach to designate specimens "informative" for qRT-PCR allowed accurate molecular assessment for the diagnosis of pancreatic diseases.

Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism

Desulfovibrio vulgaris is a metabolically flexible micro-organism. It can use sulfate as an electron acceptor to catabolize a variety of substrates, or in the absence of sulfate can utilize organic acids and alcohols by forming a syntrophic association with a hydrogen-scavenging partner to relieve inhibition by hydrogen. These alternative metabolic types increase the chance of survival for D. vulgaris in environments where one of the potential external electron acceptors becomes depleted. In this work, whole-genome D. vulgaris microarrays were used to determine relative transcript levels as D. vulgaris shifted its metabolism from syntrophic in a lactate-oxidizing dual-culture with Methanosarcina barkeri to a sulfidogenic metabolism. Syntrophic dual-cultures were grown in two independent chemostats and perturbation was introduced after six volume changes with the addition of sulfate. The results showed that 132 genes were differentially expressed in D. vulgaris 2 h after addition of sulfate. Functional analyses suggested that genes involved in cell envelope and energy metabolism were the most regulated when comparing syntrophic and sulfidogenic metabolism. Upregulation was observed for genes encoding ATPase and the membrane-integrated energy-conserving hydrogenase (Ech) when cells shifted to a sulfidogenic metabolism. A five-gene cluster encoding several lipoproteins and membrane-bound proteins was downregulated when cells were shifted to a sulfidogenic metabolism. Interestingly, this gene cluster has orthologues found only in another syntrophic bacterium, Syntrophobacter fumaroxidans, and four recently sequenced Desulfovibrio strains. This study also identified several novel c-type cytochrome-encoding genes, which may be involved in the sulfidogenic metabolism.

Hot Transcriptomics

DNA microarray technology allows for a quick and easy comparison of complete transcriptomes, resulting in improved molecular insight in fluctuations of gene expression. After emergence of the microarray technology about a decade ago, the technique has now matured and has become routine in many molecular biology laboratories. Numerous studies have been performed that have provided global transcription patterns of many organisms under a wide range of conditions. Initially, implementation of this high-throughput technology has lead to high expectations for ground breaking discoveries. Here an evaluation is performed of the insight that transcriptome analysis has brought about in the field of hyperthermophilic archaea. The examples that will be discussed have been selected on the basis of their impact, in terms of either biological insight or technological progress.

The isocitrate dehydrogenase gene of oleaginous yeast Lipomyces starkeyi is linked to lipid accumulation

The oleaginous yeast Lipomyces starkeyi can accumulate intracellular lipids to over 60% of its cell dry mass under a nitrogen-limited condition. We showed that extracellular and intracellular citrate concentrations of L. starkeyi AS 2.1560 increased and the nicotinamide adenine dinucleotide – isocitrate dehydrogenase (NAD+–IDH) activity decreased at the beginning of the lipid accumulation, suggesting that the attenuation of the NAD+–IDH activity might initiate lipid storage. We next cloned the IDH gene by the methods of degenerate PCR and rapid amplification of cDNA ends. Phylogenetic analyses of the evolutionary relationships among LsIDH1, LsIDH2, and other yeast NAD+–IDHs revealed that the L. starkeyi IDH had a closer relationship with the IDHs of Yarrowia lipolytica . Further real-time PCR analysis showed that the expression levels of both LsIDH1 and LsIDH2 decreased concurrently with the evolution of cellular lipids. Our data should be valuable for understanding the biology of oleaginous yeasts and for further strain engineering of L. starkeyi.

Preferential reduction of the thermodynamically less favorable electron acceptor, sulfate, by a nitrate-reducing strain of the sulfate-reducing bacterium Desulfovibrio desulfuricans 27774

Desulfovibrio desulfuricans strain 27774 is one of a relative small group of sulfate-reducing bacteria that can also grow with nitrate as an alternative electron acceptor, but how nitrate reduction is regulated in any sulfate-reducing bacterium is controversial. Strain 27774 grew more rapidly and to higher yields of biomass with nitrate than with sulfate or nitrite as the only electron acceptor. In the presence of both sulfate and nitrate, sulfate was used preferentially, even when cultures were continuously gassed with nitrogen and carbon dioxide to prevent sulfide inhibition of nitrate reduction. The napC transcription start site was identified 112 bases upstream of the first base of the translation start codon. Transcripts initiated at the napC promoter that were extended across the napM-napA boundary were detected by reverse transcription-PCR, confirming that the six nap genes can be cotranscribed as a single operon. Real-time PCR experiments confirmed that nap operon expression is regulated at the level of mRNA transcription by at least two mechanisms: nitrate induction and sulfate repression. We speculate that three almost perfect inverted-repeat sequences located upstream of the transcription start site might be binding sites for one or more proteins of the CRP/FNR family of transcription factors that mediate nitrate induction and sulfate repression of nitrate reduction by D. desulfuricans.

Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress

The application of DNA microarray technology to investigate multiple-species microbial communities presents great challenges. In this study, we reported the design and quality assessment of four whole genome oligonucleotide microarrays for two syntroph bacteria, Desulfovibrio vulgaris and Syntrophobacter fumaroxidans, and two archaeal methanogens, Methanosarcina barkeri, and Methanospirillum hungatei, and their application to analyze global gene expression in a four-species microbial community in response to oxidative stress. In order to minimize the possibility of cross-hybridization, cross-genome comparison was performed to assure all probes unique to each genome so that the microarrays could provide species-level resolution. Microarray quality was validated by the good reproducibility of experimental measurements of multiple biological and analytical replicates. This study showed that S. fumaroxidans and M. hungatei responded to the oxidative stress with up-regulation of several genes known to be involved in reactive oxygen species (ROS) detoxification, such as catalase and rubrerythrin in S. fumaroxidans and thioredoxin and heat shock protein Hsp20 in M. hungatei. However, D. vulgaris seemed to be less sensitive to the oxidative stress as a member of a four-species community, since no gene involved in ROS detoxification was up-regulated. Our work demonstrated the successful application of microarrays to a multiple-species microbial community, and our preliminary results indicated that this approach could provide novel insights on the metabolism within microbial communities.