Publications – David Stern
Removing systemic barriers to equity, diversity, and inclusion: Report of the 2019 Plant Science Research Network workshop “Inclusivity in the Plant Sciences”
2022.
Plant Direct.
6
:
Rubisco production in maize mesophyll cells through ectopic expression of subunits and chaperones
2021.
J Exp Bot..
:
CFM1, a Member of the CRM-domain Protein Family, Functions in Chloroplast Group II Intron Splicing in Setaria viridis
2020.
:
Plant science decadal vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future
2020.
Plant Direct..
4
:
Setaria viridis chlorotic and seedling-lethal mutants define critical functions for chloroplast gene expression
2020.
Plant J..
:
Systematic Sequencing of Chloroplast Transcript Termini From Arabidopsis Thaliana Reveals >200 Transcription Initiation Sites and the Extensive Imprints of RNA-binding Proteins and Secondary Structures
2020.
Nucelic Acids Res..
:
Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression.
2020.
Plants.
9(3)
:
Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures
2019.
Nucleic Acids Research.
47
:11889–11905
Increased Rubisco content in maize mitigates chilling stress and speeds recovery
2019.
Plant Biotechnology Journal.
:1–12
Directions for research and training in plant omics: Big Questions and Big Data
2019.
Plant Direct.
:
Overexpression of Rubisco subunits with RAF1 increases Rubisco content in maize
2018.
Nature Plants.
4
:802–810
Reinventing postgraduate training in the plant sciences: T‐training defined through modularity, customization, and distributed mentorship
2018.
Plant Direct.
2
:e00095
A Guide to the Chloroplast Transcriptome Analysis Using RNA-Seq
2018.
The Nucleus (Methods in Molecular Biology).
1829
:295–313
High‐throughput droplet microfluidics screening platform for selecting fast‐growing and high lipid‐producing microalgae from a mutant library
2017.
Plant Direct.
1
:e00011
The Rubisco Chaperone BSD2 May Regulate Chloroplast Coverage in Maize Bundle Sheath Cells
2017.
Plant Physiology.
175
:pp.01346.2017–pp.01346.2017
Selecting high-growth/high-lipid producing microalgae from a mutant library through droplet microfluidics
2016.
:
200–201
ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress
2016.
G3: Genes|Genomes|Genetics.
6
:2817–2827
Activation of an Endoribonuclease by Non-intein Protein Splicing
2016.
Journal of Biological Chemistry.
291
:15911–15922
Arabidopsis Chloroplast Mini-Ribonuclease III Participates in rRNA Maturation and Intron Recycling
2015.
The Plant Cell.
27
:724–740
A protein with an inactive pterin-4a-carbinolamine dehydratase domain is required for Rubisco biogenesis in plants
2014.
The Plant Journal.
80
:862–869
The Plant Science Decadal Vision: Response to the Martin Commentary
2013.
The Plant Cell.
25
:4775–4776
RNase J participates in a pentatricopeptide repeat protein-mediated 5′ end maturation of chloroplast mRNAs
2013.
Nucleic Acids Research.
41
:9141–9151
Setaria viridis Transformation Provides a Useful Tool for Maize Functional Genomics
2013.
IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL.
49
:S63–S64
Strand-specific RNA sequencing uncovers chloroplast ribonuclease functions
2013.
Febs Letters.
587
:3096–3101
Ribonuclease II preserves chloroplast RNA homeostasis by increasing mRNA decay rates, and cooperates with polynucleotide phosphorylase in 3 ‘ end maturation
2012.
The Plant Journal.
72
:960–971
Ribulose-1,5-Bis-Phosphate Carboxylase/Oxygenase Accumulation Factor1 Is Required for Holoenzyme Assembly in Maize
2012.
The Plant Cell.
24
:3435–3446
Ectopic Expression of Rubisco Subunits in Maize Mesophyll Cells Does Not Overcome Barriers to Cell Type-Specific Accumulation
2012.
Plant Physiology.
160
:419–432
Plastid non-coding RNAs: Emerging candidates for gene regulation
2012.
Trends in Plant Science.
17
:737–744
Overaccumulation of the chloroplast antisense RNA AS5 is correlated with decreased abundance of 5S rRNA in vivo and inefficient 5S rRNA maturation in vitro
2011.
RNA (New York, N.Y.).
17
:230–243
Mutational analysis of Arabidopsis chloroplast polynucleotide phosphorylase reveals roles for both RNase PH core domains in polyadenylation, RNA 3 ‘-end maturation and intron degradation
2011.
The Plant Journal.
67
:381–394
Chloroplast RNase J compensates for inefficient transcription termination by removal of antisense RNA
2011.
RNA (New York, N.Y.).
17
:2165–2176
Developmental and cell type characterization of bundle sheath and mesophyll chloroplast transcript abundance in maize
2011.
Current Genetics.
57
:89–102
Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome
2011.
G3: Genes|Genomes|Genetics.
1
:559–570
Transgenic maize lines with cell-type specific expression of fluorescent proteins in plastids
2010.
Plant Biotechnology Journal.
8
:112–125
MRL1, a Conserved Pentatricopeptide Repeat Protein, Is Required for Stabilization of rbcL mRNA in Chlamydomonas and Arabidopsis
2010.
The Plant Cell.
22
:234–248
Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize
2010.
The Plant Journal.
63
:167–177
Differential Replication of Two Chloroplast Genome Forms in Heteroplasmic Chlamydomonas reinhardtii Gametes Contributes to Alternative Inheritance Patterns
2010.
Genetics.
185
:1167–1181
Overexpression of a natural chloroplast-encoded antisense RNA in tobacco destabilizes 5S rRNA and retards plant growth
2010.
BMC Plant Biology.
10
:213–213
Insights into the Evolution of Mitochondrial Genome Size from Complete Sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae)
2010.
Molecular Biology and Evolution.
27
:1436–1448
Polyadenylation in Arabidopsis and Chlamydomonas organelles: The input of nucleotidyltransferases, poly(A)-polymerases and polynucleotide phosphorylase
2009.
The Plant Journal.
59
:88–89
Mating and Tetrad Separation of Chlamydomonas reinhardtii for Genetic Analysis
2009.
Journal of visualized experiments : JoVE.
:96–101
The RNA-binding proteins CSP41a and CSP41b may regulate transcription and translation of chloroplast-encoded RNAs in Arabidopsis
2009.
Plant Molecular Biology.
69
:541–552
Abnormal Physiological and Molecular Mutant Phenotypes Link Chloroplast Polynucleotide Phosphorylase to the Phosphorus Deprivation Response in Arabidopsis
2009.
Plant Physiology.
151
:905–924
Nuclear, chloroplast, and mitochondrial transcript abundance along a maize leaf developmental gradient
2008.
Plant Molecular Biology.
66
:33–46
MEMS based bioelectronic neuromuscular interfaces for insect cyborg flight control
2008.
MEMS 2008: 21ST IEEE INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS, TECHNICAL DIGEST.
:160–163
Genome-Based Analysis of Chlamydomonas reinhardtii Exoribonucleases and Poly(A) Polymerases Predicts Unexpected Organellar and Exosomal Features
2008.
Genetics.
179
:125–136
Rubisco large-subunit translation is autoregulated in response to its assembly state in tobacco chloroplasts
2007.
Proceedings of the National Academy of Sciences.
104
:6466–6471
Antisense transcript suppress instability of polyadenylated mRNA in Chlamydomonas chloroplasts
2007.
PLANT AND CELL PHYSIOLOGY.
48
:S37–S37
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions
2007.
Science.
318
:245–251
Processing, degradation, and polyadenylation of chloroplast transcripts
2007.
Topics in Current Genetics.
19
:175–211
The nucleus-encoded factor MCD4 participates in degradation of nonfunctional 3 ‘ UTR sequences generated by cleavage of pre-mRNA in Chlamydomonas chloroplasts
2007.
Molecular genetics and genomics : MGG.
277
:329–340
Chlamydomonas reinhardtii encodes a single sigma70-like factor which likely functions in chloroplast transcription
2006.
Current Genetics.
49
:333–340
Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach
2006.
BMC Evolutionary Biology.
6
:
Nuclear suppressors define three factors that participate in both 5 ‘ and 3 ‘ end processing of mRNAs in Chlamydomonas chloroplasts
2006.
The Plant Journal.
46
:448–461
The sulfur acclimation SAC3 kinase is required for chloroplast transcriptional repression under sulfur limitation in Chlamydomonas reinhardtii
2006.
Proceedings of the National Academy of Sciences.
103
:7911–7916
A spontaneous tRNA suppressor of a mutation in the Chlamydomonas reinhardtii nuclear MCD1 gene required for stability of the chloroplast petD mRNA
2005.
Nucleic Acids Research.
33
:3372–3380
Microarray Analysis Confirms the Specificity of a Chlamydomonas reinhardtii Chloroplast RNA Stability Mutant
2005.
Plant Physiology.
137
:534–544
Beyond Complementation. Map-Based Cloning in Chlamydomonas reinhardtii
2005.
Plant Physiology.
137
:557–566
RNR1, a 3 ‘-5 ‘ exoribonuclease belonging to the RNR superfamily, catalyzes 3 ‘ maturation of chloroplast ribosomal RNAs in Arabidopsis thaliana
2005.
Nucleic Acids Research.
33
:2751–2763
Short dispersed repeats in the Chlamydomonas chloroplast genome are collocated with sites for mRNA 3 ‘ end formation
2004.
Current Genetics.
45
:311–322
Cooperation of Endo- and Exoribonucleases in Chloroplast mRNA Turnover
2004.
PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY, VOL 78.
78
:305–337
Antisense Transcript and RNA Processing Alterations Suppress Instability of Polyadenylated mRNA in Chlamydomonas Chloroplasts
2004.
The Plant Cell.
16
:2849–2869
Analysis of developing maize plastids reveals two mRNA stability classes correlating with RNA polymerase type
2004.
EMBO Journal.
5
:801–806
In vivo evidence for the prokaryotic model of extended codon-anticodon interaction in translation initiation
2003.
The EMBO Journal.
22
:651–656
Divalent metal-dependent catalysis and cleavage specificity of CSP41, a chloroplast endoribonuclease belonging to the short chain dehydrogenase/reductase superfamily
2003.
Nucleic Acids Research.
31
:4317–4325
CSP41a, a multifunctional RNA-binding protein, initiates mRNA turnover in tobacco chloroplasts
2003.
The Plant Journal.
36
:842–852
Secondary Structures Common to Chloroplast mRNA 3′-Untranslated Regions Direct Cleavage by CSP41, an Endoribonuclease Belonging to the Short Chain Dehydrogenase/Reductase Superfamily
2003.
Journal of Biological Chemistry.
278
:25832–25838
The Plastid clpP Gene May Not be Essential for Plant Cell Viability
2003.
Plant and Cell Physiology.
44
:93–95
Maize BMS cultured cell lines survive with massive plastid gene loss
2003.
Current Genetics.
44
:104–113
A nucleus-encoded maize protein with sigma factor activity accumulates in mitochondria and chloroplasts
2002.
The Plant Journal.
31
:199–209
Evidence for in vivo modulation of chloroplast RNA stability by 3 ‘-UTR homopolymeric tails in Chlamydomonas reinhardtii
2002.
Proceedings of the National Academy of Sciences.
99
:4085–4090
The Treasure Trove of Algal Chloroplast Genomes. Surprises in Architecture and Gene Content, and Their Functional Implications
2002.
Plant Physiology.
129
:957–966
A dominant nuclear mutation in Chlamydomonas identifies a factor controlling chloroplast mRNA stability by acting on the coding region of the atpA transcript
2002.
The Plant Journal.
31
:687–697
An mRNA 3′ Processing Site Targets Downstream Sequences for Rapid Degradation in Chlamydomonas Chloroplasts
2002.
Journal of Biological Chemistry.
277
:3325–3333
The Chlamydomonas reinhardtti plastid chromosome: Islands of genes in a sea of repeats
2002.
The Plant Cell.
14
:2659–2679
Chlamydomonas reinhardtii as a model system for dissecting chloroplast RNA processing and decay mechanisms
2001.
Methods in Enzymology, Vol 469: Biophysical, Chemical, and Functional Probes of Rna Structure, Interactions and Folding, Pt B.
342
:384–407
A Role for Initiation Codon Context in Chloroplast Translation
2001.
The Plant Cell.
13
:2373–2384
A nucleus-encoded suppressor defines a new factor which can promote petD mRNA stability in the chloroplast of Chlamydomonas reinhardtii
2001.
Current Genetics.
39
:40–48
The Chloroplast Gene ycf9 Encodes a Photosystem II (PSII) Core Subunit, PsbZ, That Participates in PSII Supramolecular Architecture
2001.
The Plant Cell.
13
:1347–1367
Post-transcriptional defects in tobacco chloroplast mutants lacking the cytochrome b6/f complex
2000.
The Plant Journal.
21
:61–72
Identification of the initiation codon for the atpB gene in Chlamydomonas chloroplasts excludes translation of a precursor form of the β subunit of the ATP synthase
2000.
Molecular and General Genetics MGG.
264
:486–491
The sequence and secondary structure of the 3 ‘-UTR affect 3 ‘-end maturation, RNA accumulation, and translation in tobacco chloroplasts
2000.
Plant Molecular Biology.
44
:529–542
Polyadenylation of three classes of chloroplast RNA in Chlamydomonas reinhardtii
2000.
RNA (New York, N.Y.).
6
:598–607
Regulation of plastid rDNA transcription by interaction of CDF2 with two different RNA polymerases
2000.
The EMBO Journal.
19
:1851–1860
Disruption of the petB-petD intergenic region in tobacco chloroplasts affects petD RNA accumulation and translation
2000.
Molecular and General Genetics MGG.
263
:610–618
The Maize Mitochondrial cox2 Gene Has Five Promoters in Two Genomic Regions, Including a Complex Promoter Consisting of Seven Overlapping Units
1999.
Journal of Biological Chemistry.
274
:3897–3903
Polyadenylation Occurs at Multiple Sites in Maize Mitochondrial cox2 mRNA and Is Independent of Editing Status
1999.
The Plant Cell.
11
:1565–1577
5 ‘ to 3 ‘ exoribonucleolytic activity is a normal component of chloroplast mRNA decay pathways
1999.
The Plant Journal.
19
:521–531
Functional Analysis of Two Maize cDNAs Encoding T7-like RNA Polymerases
1999.
The Plant Cell.
11
:911–926
DNA-binding factors assemble in a sequence-specific manner on the maize mitochondrial atpA promoter
1999.
Current Genetics.
35
:506–511
Target and Specificity of a Nuclear Gene Product That Participates in mRNA 3′-End Formation in Chlamydomonas Chloroplasts
1999.
Journal of Biological Chemistry.
274
:35955–35962
Altering the 3 ‘ UTR endonucleolytic cleavage site of a Chlamydomonas chloroplast mRNA affects 3 ‘-end maturation in vitro but not in vivo
1999.
Plant Molecular Biology.
40
:679–686
Small cis -Acting Sequences That Specify Secondary Structures in a Chloroplast mRNA Are Essential for RNA Stability and Translation
1999.
Molecular and Cellular Biology.
19
:8479–8491
Genomic context influences the activity of maize mitochondrial cox2 promoters
1999.
Proceedings of the National Academy of Sciences.
96
:11670–11675
In vivo evidence for 5 ‘-> 3 ‘ exoribonuclease degradation of an unstable chloroplast mRNA
1998.
The Plant Journal.
13
:85–96
Inversions in the Chlamydomonas chloroplast genome suppress a petD 5 ‘ untranslated region deletion by creating functional chimeric mRNAs
1998.
The Plant Journal.
14
:663–671
3′-Processed mRNA Is Preferentially Translated in Chlamydomonas reinhardtii Chloroplasts
1998.
Molecular and Cellular Biology.
18
:4605–4611
The chloroplast atpA gene cluster in Chlamydomonas reinhardtii. Functional analysis of a polycistronic transcription unit
1998.
Plant Physiology.
117
:629–641
The sequence and structure of the 3 ‘-untranslated regions of chloroplast transcripts are important determinants of mRNA accumulation and stability
1998.
Plant Molecular Biology.
36
:307–314
Translation of cytochrome f is autoregulated through the 5 ‘ untranslated region of petA mRNA in Chlamydomonas chloroplasts
1998.
Proceedings of the National Academy of Sciences.
95
:4380–4385
A conserved core element is functionally important for maize mitochondrial promoter activity in vitro
1997.
Nucleic Acids Research.
25
:4055–4060
Transcriptional activities of maize mitochondria
1997.
Plant Physiology.
114
:1012–1012
Generation and maintenance of tandemly repeated extrachromosomal plasmid DNA in Chlamydomonas chloroplasts
1997.
The Plant Journal.
11
:635–648
A Nuclear Mutation That Affects the 3[prime] Processing of Several mRNAs in Chlamydomonas Chloroplasts
1997.
The Plant Cell.
9
:825–836
Ccs1 , a Nuclear Gene Required for the Post-translational Assembly of Chloroplast c -Type Cytochromes
1997.
Journal of Biological Chemistry.
272
:31747–31754
The Spinach Chloroplast Endoribonuclease CSP41 Cleaves the 3′-Untranslated Region of petD mRNA Primarily within Its Terminal Stem-Loop Structure
1997.
Journal of Biological Chemistry.
272
:12874–12880
A dominant mutation in the Chlamydomonas reinhardtii nuclear gene SIM30 suppresses translational defects caused by initiation codon mutations in chloroplast genes
1997.
Genetics.
145
:935–943
CSP41, a Sequence-Specific Chloroplast mRNA Binding Protein, Is an Endoribonuclease
1996.
The Plant Cell.
8
:1409–1420
The 3′ untranslated regions of chloroplast genes in Chlamydomonas reinhardtii do not serve as efficient transcriptional terminators
1996.
Molecular and General Genetics MGG.
252
:676–683
A chloroplast transcript lacking the 3′ inverted repeat is degraded by 3′ → 5′ exoribonuclease activity
1996.
RNA (New York, N.Y.).
2
:652–663
Mitochondrial transcription initiation: promoter structures and RNA polymerases
1995.
Current Genetics.
28
:205–216
An AU-rich element in the 3′ untranslated region of the spinach chloroplast petD gene participates in sequence-specific RNA-protein complex formation
1995.
Molecular and Cellular Biology.
15
:2010–2018
Evidence for a novel mitochondrial promoter preceding the cox2 gene of perennial teosintes
1995.
The EMBO Journal.
14
:585–593
The 41 kDa protein component of the spinach chloroplast petD mRNA 3′ stem-loop:protein complex is a nuclear encoded chloroplast RNA-binding protein
1995.
Nucleic acids symposium series.
:237–239
The Initiation Codon Determines the Efficiency but Not the Site of Translation Initiation in Chlamydomonas Chloroplasts
1995.
The Plant Cell.
7
:1295–1305
The petD gene is transcribed by functionally redundant promoters in Chlamydomonas reinhardtii chloroplasts
1994.
Molecular and Cellular Biology.
14
:6171–6179
INTERACTIONS OF CHLOROPLAST MESSENGER-RNA 3′ UNTRANSLATED REGIONS WITH PROTEINS THAT PROMOTE RNA PROCESSING AND STABILITY
1994.
JOURNAL OF CELLULAR BIOCHEMISTRY.
:149–149
Gene Amplification Can Correct a Photosynthetic Growth Defect Caused by mRNA Instability in Chlamydomonas Chloroplasts
1994.
The Plant Cell.
6
:187–200
petD mRNA maturation in Chlamydomonas reinhardtii chloroplasts: Role of 5′ endonucleolytic processing
1994.
Molecular and Cellular Biology.
14
:6180–6186
Function of the Chlamydomonas reinhardtii petD 5′ untranslated region in regulating the accumulation of subunit IV of the cytochrome b6/f complex
1994.
The Plant Journal.
6
:503–512
Architecture of the maize mitochondrial atp1 promoter as determined by linker-scanning and point mutagenesis
1993.
Molecular and Cellular Biology.
13
:7232–7238
Initiation codon mutations in the Chlamydomonas chloroplast petD gene result in temperature-sensitive photosynthetic growth
1993.
The EMBO Journal.
12
:3627–3635
3′ end maturation of the Chlamydomonas reinhardtii chloroplast atpB mRNA is a two-step process
1993.
Molecular and Cellular Biology.
13
:2277–2285
A conserved 11 nucleotide sequence contains an essential promoter element of the maize mitochondrial atp1 gene
1992.
The EMBO Journal.
11
:1065–1073
Specific binding of chloroplast proteins in vitro to the 3′ untranslated region of spinach chloroplast petD mRNA
1991.
Molecular and Cellular Biology.
11
:4380–4388
Engineering the chloroplast genome: Techniques and capabilities for chloroplast transformation in Chlamydomonas reinhardtii
1991.
Proceedings of the National Academy of Sciences.
88
:1721–1725
Specific ribonuclease activities in spinach chloroplasts promote mRNA maturation and degradation
1991.
Journal of Biological Chemistry.
266
:24205–24211
A 3[prime] Stem/Loop Structure of the Chlamydomonas Chloroplast atpB Gene Regulates mRNA Accumulation in Vivo
1991.
The Plant Cell.
3
:285–297
Control of mRNA stability in chloroplasts by 3′ inverted repeats: Effects of stem and loop mutations on degradation of PsbA mRNA in vitro
1990.
Nucleic Acids Research.
18
:6003–6010
Chloroplast mRNA 3? end maturation is biochemically distinct from prokaryotic mRNA processing
1989.
Plant Molecular Biology.
13
:615–625
Function of plastid mRNA 3′ inverted repeats. RNA stabilization and gene-specific protein binding
1989.
Journal of Biological Chemistry.
264
:18742–18750
Transcriptional and post-transcriptional control of plastid mRNA levels in higher plants
1988.
Trends in genetics : TIG.
4
:258–263
Control of plastid gene expression: 3′ inverted repeats act as mRNA processing and stabilizing elements, but do not terminate transcription
1987.
Cell.
51
:1145–1157
Plastid run-on transcription. Application to determine the transcriptional regulation of spinach plastid genes
1987.
Journal of Biological Chemistry.
262
:9641–9648
DNA transposition between plant organellar genomes
1987.
Journal of cell science. Supplement.
7
:145–154
Isolation of plant mitochondrial RNA
1986.
Methods in Enzymology, Vol 469: Biophysical, Chemical, and Functional Probes of Rna Structure, Interactions and Folding, Pt B.
118
:488–496
The watermelon mitochondrial URF-1 gene: evidence for a complex structure
1986.
Current Genetics.
10
:857–869
Isolation of intact plant mitochondrial RNA using aurintricarboxylic acid
1984.
Plant Molecular Biology Reporter.
2
:8–15
Homology between the ribosomal DNA of Escherichia coli and mitochondrial DNA preparations of maize is principally to sequences other than mitochondrial rRNA genes
1984.
Plant Molecular Biology.
3
:355–361
Recombination sequences in plant mitochondrial genomes: Diversity and homologies to known mitochondrial genes
1984.
Nucleic Acids Research.
12
:6141–6157
Extensive and widespread homologies between mitochondrial DNA and chloroplast DNA in plants
1984.
Proceedings of the National Academy of Sciences.
81
:1946–1950
Organization of the mitochondrial ribosomal RNA genes of maize
1982.
Nucleic Acids Research.
10
:3333–3340
Mitochondrial and chloroplast genomes of maize have a 12-kilobase DNA sequence in common
1982.
Nature.
299
:698–702
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